11-17474969-A-G

Position:

• chr11-17474969-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BA1

The NM_000352.6(ABCC8):​c.207T>C​(p.Pro69=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,613,814 control chromosomes in the GnomAD database, including 191,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.46 (16400 hom., cov: 32)
  • Exomes 𝑓: 0.49 (175359 hom.)
• Consequence: ABCC8 NM_000352.6 synonymous
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:16
• Conservation: PhyloP100: -2.61

Genes affected

ABCC8 (HGNC:59): (ATP binding cassette subfamily C member 8) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MRP subfamily which is involved in multi-drug resistance. This protein functions as a modulator of ATP-sensitive potassium channels and insulin release. Mutations in the ABCC8 gene and deficiencies in the encoded protein have been observed in patients with hyperinsulinemic hypoglycemia of infancy, an autosomal recessive disorder of unregulated and high insulin secretion. Mutations have also been associated with non-insulin-dependent diabetes mellitus type II, an autosomal dominant disease of defective insulin secretion. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2020]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 11-17474969-A-G is Benign according to our data. Variant chr11-17474969-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 157687.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1, Benign=12}. Variant chr11-17474969-A-G is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=-2.61 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC8	NM_000352.6	c.207T>C	p.Pro69=	synonymous_variant	2/39	ENST00000389817.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC8	ENST00000389817.8	c.207T>C	p.Pro69=	synonymous_variant	2/39	1	NM_000352.6	P4

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69831 AN: 151940 Hom.: 16402 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.512

GnomAD3 exomes AF: 0.475 AC: 119354 AN: 251110 Hom.: 29196 AF XY: 0.475 AC XY: 64432 AN XY: 135742

Gnomad AFR exome AF: 0.396

Gnomad AMR exome AF: 0.565

Gnomad ASJ exome AF: 0.549

Gnomad EAS exome AF: 0.363

Gnomad SAS exome AF: 0.465

Gnomad FIN exome AF: 0.322

Gnomad NFE exome AF: 0.502

Gnomad OTH exome AF: 0.490

GnomAD4 exome AF: 0.487 AC: 711716 AN: 1461760 Hom.: 175359 Cov.: 64 AF XY: 0.487 AC XY: 353913 AN XY: 727182

Gnomad4 AFR exome AF: 0.402

Gnomad4 AMR exome AF: 0.562

Gnomad4 ASJ exome AF: 0.543

Gnomad4 EAS exome AF: 0.376

Gnomad4 SAS exome AF: 0.469

Gnomad4 FIN exome AF: 0.326

Gnomad4 NFE exome AF: 0.498

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.459 AC: 69856 AN: 152054 Hom.: 16400 Cov.: 32 AF XY: 0.452 AC XY: 33561 AN XY: 74324

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.508

Alfa AF: 0.489 Hom.: 20845

Bravo AF: 0.474

Asia WGS AF: 0.393 AC: 1365 AN: 3478

EpiCase AF: 0.524

EpiControl AF: 0.533

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:16

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Benign:5

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 07, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 14, 2014	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

not provided Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2018	This variant is associated with the following publications: (PMID: 21671119) -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 12, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

Hyperinsulinemic hypoglycemia, familial, 1 Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Pars Genome Lab	Jul 01, 2021	- -

Diabetes mellitus, transient neonatal, 2 Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Pars Genome Lab	Jul 01, 2021	- -

Hyperinsulinemia Uncertain:1

Uncertain significance, criteria provided, single submitter

research

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

-

Mutations in ABCC8 gene are generally associated with both neonatal diabetes mellitus as well as MODY. Patients with this mutation may respond to sulfonylureas. Although rs1048099 is prevalent in hyperinsulinemic hypoglycemia in infancy, sufficient evidence is not seen to demonstrate the association of this variant with neonatal diabetes or MODY. -

Hereditary hyperinsulinism Benign:1

Benign, no assertion criteria provided

clinical testing

Natera, Inc.

Sep 16, 2020

- -

Leucine-induced hypoglycemia Benign:1

Benign, criteria provided, single submitter

clinical testing

Pars Genome Lab

Jul 01, 2021

- -

Diabetes mellitus, permanent neonatal 3 Benign:1

Benign, criteria provided, single submitter

clinical testing

Pars Genome Lab

Jul 01, 2021

- -

Permanent neonatal diabetes mellitus Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.61
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1048099; hg19: chr11-17496516; COSMIC: COSV56850629;