rs2402941

Variant names:

• chr7-128922960-A-G
• rs2402941

Your query was ambiguous. Multiple possible variants found:

• chr7-128922960-A-G
• chr7-128922960-A-T

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 0.775 in 152,086 control chromosomes in the GnomAD database, including 46,789 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 (46789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.853 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: 0.775 AC: 117846 AN: 151966 Hom.: 46776 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.775 AC: 117905 AN: 152086 Hom.: 46789 Cov.: 31 AF XY: 0.776 AC XY: 57665 AN XY: 74340

African (AFR) AF: 0.625 AC: 25932 AN: 41466

American (AMR) AF: 0.746 AC: 11409 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3152 AN: 3472

East Asian (EAS) AF: 0.573 AC: 2949 AN: 5148

South Asian (SAS) AF: 0.833 AC: 4010 AN: 4816

European-Finnish (FIN) AF: 0.878 AC: 9316 AN: 10606

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58407 AN: 67968

Other (OTH) AF: 0.771 AC: 1629 AN: 2114

Alfa AF: 0.806 Hom.: 24451

Bravo AF: 0.756

Asia WGS AF: 0.710 AC: 2468 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	3.9
DANN	Benign	0.67
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs2402941; hg19: chr7-128563014;