rs4943389

Variant names:

• chr13-36536762-A-C
• rs4943389

Your query was ambiguous. Multiple possible variants found:

• chr13-36536762-A-C
• chr13-36536762-A-G
• chr13-36536762-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;