rs4943389

chr13-36536762-A-Cchr13-36536762-A-Gchr13-36536762-A-T

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 0.588 in 151,720 control chromosomes in the GnomAD database, including 26,886 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 0.59 (26886 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.588 AC: 89138 AN: 151602 Hom.: 26874 Cov.: 31

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.588 AC: 89196 AN: 151720 Hom.: 26886 Cov.: 31 AF XY: 0.593 AC XY: 43964 AN XY: 74156

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.567

Alfa AF: 0.590 Hom.: 6663

Bravo AF: 0.589

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943389; hg19: chr13-37110899;