chr5-79533426-A-G

Variant names:

• chr5-79533426-A-G
• rs7713917

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 0.531 in 152,164 control chromosomes in the GnomAD database, including 24,103 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 0.53 (24103 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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: 0.530 AC: 80646 AN: 152044 Hom.: 24050 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.531 AC: 80764 AN: 152164 Hom.: 24103 Cov.: 33 AF XY: 0.535 AC XY: 39779 AN XY: 74378

African (AFR) AF: 0.801 AC: 33272 AN: 41526

American (AMR) AF: 0.550 AC: 8405 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3468

East Asian (EAS) AF: 0.632 AC: 3279 AN: 5188

South Asian (SAS) AF: 0.351 AC: 1692 AN: 4816

European-Finnish (FIN) AF: 0.534 AC: 5649 AN: 10582

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25665 AN: 67994

Other (OTH) AF: 0.496 AC: 1045 AN: 2108

Alfa AF: 0.420 Hom.: 67819

Bravo AF: 0.551

Asia WGS AF: 0.533 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.77
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7713917; hg19: chr5-78829249; COSMIC: COSV65983187;