rs2477601

chr13-46332739-G-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 0.223 in 148,276 control chromosomes in the GnomAD database, including 3,943 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 0.22 (3943 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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: 0.223 AC: 33076 AN: 148188 Hom.: 3931 Cov.: 28

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.223 AC: 33110 AN: 148276 Hom.: 3943 Cov.: 28 AF XY: 0.221 AC XY: 15972 AN XY: 72114

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.212

Alfa AF: 0.223 Hom.: 775

Bravo AF: 0.228

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.80
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2477601; hg19: chr13-46906874;