3-7796555-G-A

Variant names:

• chr3-7796555-G-A
• rs161927

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 0.808 in 151,972 control chromosomes in the GnomAD database, including 50,416 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 0.81 (50416 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122750 AN: 151854 Hom.: 50391 Cov.: 30

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.808 AC: 122835 AN: 151972 Hom.: 50416 Cov.: 30 AF XY: 0.813 AC XY: 60385 AN XY: 74268

African (AFR) AF: 0.649 AC: 26884 AN: 41396

American (AMR) AF: 0.842 AC: 12860 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2994 AN: 3472

East Asian (EAS) AF: 0.957 AC: 4925 AN: 5148

South Asian (SAS) AF: 0.908 AC: 4373 AN: 4814

European-Finnish (FIN) AF: 0.885 AC: 9352 AN: 10572

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.863 AC: 58650 AN: 67976

Other (OTH) AF: 0.817 AC: 1728 AN: 2114

Alfa AF: 0.853 Hom.: 84571

Bravo AF: 0.797

Asia WGS AF: 0.893 AC: 3105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.012
DANN	Benign	0.42
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs161927; hg19: chr3-7838242;