rs563630291

Positions:

• chr11-2161296-TG-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_Strong BS2

The variant allele was found at a frequency of 0.0104 in 318,044 control chromosomes in the GnomAD database, including 28 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0097 (10 hom., cov: 33)
  • Exomes 𝑓: 0.011 (18 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -2.66

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP6: Variant 11-2161296-TG-T is Benign according to our data. Variant chr11-2161296-TG-T is described in ClinVar as [Benign]. Clinvar id is 435506.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2161297delG		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00967 AC: 1470 AN: 152010 Hom.: 10 Cov.: 33

Gnomad AFR AF: 0.00210

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.00714

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.00860

GnomAD4 exome AF: 0.0110 AC: 1833 AN: 165916 Hom.: 18 Cov.: 0 AF XY: 0.0109 AC XY: 913 AN XY: 83750

Gnomad4 AFR exome AF: 0.00238

Gnomad4 AMR exome AF: 0.00497

Gnomad4 ASJ exome AF: 0.000333

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00535

Gnomad4 FIN exome AF: 0.0260

Gnomad4 NFE exome AF: 0.0134

Gnomad4 OTH exome AF: 0.00988

GnomAD4 genome AF: 0.00966 AC: 1469 AN: 152128 Hom.: 10 Cov.: 33 AF XY: 0.0103 AC XY: 764 AN XY: 74384

Gnomad4 AFR AF: 0.00210

Gnomad4 AMR AF: 0.00713

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00311

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0138

Gnomad4 OTH AF: 0.00851

Alfa AF: 0.0110 Hom.: 3

Bravo AF: 0.00762

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 25, 2019	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2024	INS-IGF2: BS1, BS2 -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Oct 31, 2016

- -

Neonatal insulin-dependent diabetes mellitus Benign:1

Benign, criteria provided, single submitter

research

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

-

Mutations in INS gene can cause early onset diabetes mellitus which is insulin dependent. May have poor response to sulfonylureas, as this mutation can cause beta cell destruction. However no sufficient evidence is found to ascertain the role of this particular variant rs563630291, yet. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs563630291; hg19: chr11-2182526;