rs12788013

Positions:

• chr11-5225365-C-G
• chr11-5225365-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000644706.1(ENSG00000285498):​n.97G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 524,032 control chromosomes in the GnomAD database, including 3,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.11 (936 hom., cov: 33)
  • Exomes 𝑓: 0.12 (2907 hom.)
• Consequence: ENST00000644706.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts P:1 B:5
• Conservation: PhyloP100: 0.0620

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 11-5225365-C-G is Benign according to our data. Variant chr11-5225365-C-G is described in ClinVar as [Benign]. Clinvar id is 256341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644706.1	n.97G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16040 AN: 152056 Hom.: 933 Cov.: 33

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.102

GnomAD4 exome AF: 0.117 AC: 43645 AN: 371858 Hom.: 2907 Cov.: 4 AF XY: 0.122 AC XY: 24259 AN XY: 199108

Gnomad4 AFR exome AF: 0.0773

Gnomad4 AMR exome AF: 0.0727

Gnomad4 ASJ exome AF: 0.0934

Gnomad4 EAS exome AF: 0.0150

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.148

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.105 AC: 16044 AN: 152174 Hom.: 936 Cov.: 33 AF XY: 0.108 AC XY: 8000 AN XY: 74388

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.0212

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0629 Hom.: 75

Bravo AF: 0.0943

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:4

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	This variant is associated with the following publications: (PMID: 26524961, 27884173, 23321370) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 29, 2023	- -

beta Thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

curation

The ITHANET community portal, The Cyprus Institute of Neurology and Genetics

Nov 25, 2019

- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12788013; hg19: chr11-5246595;