rs567926

Variant names:

• chr4-46239752-G-A
• rs567926

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.631

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs567926; hg19: chr4-46241769;