rs7628767

Variant names:

• chr3-103681238-G-A
• rs7628767

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 0.453 in 151,618 control chromosomes in the GnomAD database, including 17,013 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 0.45 (17013 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68613 AN: 151500 Hom.: 16969 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.453 AC: 68720 AN: 151618 Hom.: 17013 Cov.: 31 AF XY: 0.461 AC XY: 34147 AN XY: 74078

African (AFR) AF: 0.641 AC: 26539 AN: 41376

American (AMR) AF: 0.481 AC: 7299 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3462

East Asian (EAS) AF: 0.563 AC: 2863 AN: 5086

South Asian (SAS) AF: 0.589 AC: 2838 AN: 4820

European-Finnish (FIN) AF: 0.388 AC: 4104 AN: 10566

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22371 AN: 67838

Other (OTH) AF: 0.462 AC: 969 AN: 2098

Alfa AF: 0.386 Hom.: 35121

Bravo AF: 0.468

Asia WGS AF: 0.642 AC: 2233 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	1.1
DANN	Benign	0.51
PhyloP100		-0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7628767;

hg19: chr3-103400082;