chr2-156696348-A-C

Variant names:

• chr2-156696348-A-C
• rs7601713

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.782 in 152,172 control chromosomes in the GnomAD database, including 46,791 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (46791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118890 AN: 152054 Hom.: 46731 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.771

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.782 AC: 119005 AN: 152172 Hom.: 46791 Cov.: 32 AF XY: 0.786 AC XY: 58481 AN XY: 74402

African (AFR) AF: 0.851 AC: 35315 AN: 41516

American (AMR) AF: 0.827 AC: 12643 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2530 AN: 3472

East Asian (EAS) AF: 0.791 AC: 4092 AN: 5172

South Asian (SAS) AF: 0.824 AC: 3978 AN: 4826

European-Finnish (FIN) AF: 0.758 AC: 8021 AN: 10582

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49864 AN: 67992

Other (OTH) AF: 0.772 AC: 1629 AN: 2110

Alfa AF: 0.754 Hom.: 143150

Bravo AF: 0.787

Asia WGS AF: 0.816 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.73
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7601713; hg19: chr2-157552860;