7-64158090-A-G

Variant names:

• chr7-64158090-A-G
• rs1529813

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 0.727 in 151,878 control chromosomes in the GnomAD database, including 40,843 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 0.73 (40843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 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: 0.727 AC: 110367 AN: 151758 Hom.: 40800 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.727 AC: 110467 AN: 151878 Hom.: 40843 Cov.: 32 AF XY: 0.724 AC XY: 53773 AN XY: 74244

African (AFR) AF: 0.848 AC: 35159 AN: 41462

American (AMR) AF: 0.715 AC: 10901 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2316 AN: 3464

East Asian (EAS) AF: 0.916 AC: 4745 AN: 5180

South Asian (SAS) AF: 0.667 AC: 3213 AN: 4816

European-Finnish (FIN) AF: 0.611 AC: 6434 AN: 10534

Middle Eastern (MID) AF: 0.697 AC: 202 AN: 290

European-Non Finnish (NFE) AF: 0.669 AC: 45397 AN: 67864

Other (OTH) AF: 0.746 AC: 1573 AN: 2108

Alfa AF: 0.703 Hom.: 9534

Bravo AF: 0.743

Asia WGS AF: 0.794 AC: 2728 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.88
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1529813; hg19: chr7-63618468;