rs567926

Variant names:

• chr4-46239752-G-A
• rs567926

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 0.626 in 151,698 control chromosomes in the GnomAD database, including 30,396 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 0.63 (30396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 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: 0.626 AC: 94884 AN: 151578 Hom.: 30354 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.626 AC: 94971 AN: 151698 Hom.: 30396 Cov.: 32 AF XY: 0.627 AC XY: 46416 AN XY: 74060

African (AFR) AF: 0.743 AC: 30775 AN: 41426

American (AMR) AF: 0.554 AC: 8434 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2405 AN: 3466

East Asian (EAS) AF: 0.546 AC: 2757 AN: 5054

South Asian (SAS) AF: 0.778 AC: 3738 AN: 4806

European-Finnish (FIN) AF: 0.592 AC: 6250 AN: 10550

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38539 AN: 67874

Other (OTH) AF: 0.631 AC: 1328 AN: 2106

Alfa AF: 0.587 Hom.: 4544

Bravo AF: 0.621

Asia WGS AF: 0.655 AC: 2277 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs567926; hg19: chr4-46241769;