rs567926

chr4-46239752-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;