rs2477601

Variant names:

• chr13-46332739-G-T
• rs2477601

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.272 AC: 10962 AN: 40258

American (AMR) AF: 0.214 AC: 3203 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 785 AN: 3452

East Asian (EAS) AF: 0.145 AC: 727 AN: 5030

South Asian (SAS) AF: 0.132 AC: 623 AN: 4734

European-Finnish (FIN) AF: 0.227 AC: 2119 AN: 9354

Middle Eastern (MID) AF: 0.264 AC: 75 AN: 284

European-Non Finnish (NFE) AF: 0.209 AC: 14079 AN: 67246

Other (OTH) AF: 0.212 AC: 437 AN: 2060

Alfa AF: 0.230 Hom.: 2472

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2477601; hg19: chr13-46906874;