rs7606972

Variant names:

• chr2-136699130-G-T
• rs7606972

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 0.658 in 152,096 control chromosomes in the GnomAD database, including 33,295 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 0.66 (33295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100107 AN: 151978 Hom.: 33295 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.658 AC: 100148 AN: 152096 Hom.: 33295 Cov.: 32 AF XY: 0.663 AC XY: 49305 AN XY: 74350

African (AFR) AF: 0.586 AC: 24316 AN: 41484

American (AMR) AF: 0.751 AC: 11486 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2610 AN: 3470

East Asian (EAS) AF: 0.736 AC: 3812 AN: 5176

South Asian (SAS) AF: 0.755 AC: 3638 AN: 4820

European-Finnish (FIN) AF: 0.672 AC: 7102 AN: 10568

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44974 AN: 67978

Other (OTH) AF: 0.667 AC: 1407 AN: 2108

Alfa AF: 0.669 Hom.: 5360

Bravo AF: 0.662

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.47
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7606972; hg19: chr2-137456700;