rs13385025

Variant names:

• chr2-62233985-G-A
• rs13385025

Your query was ambiguous. Multiple possible variants found:

• chr2-62233985-G-A
• chr2-62233985-G-C
• chr2-62233985-G-T

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 0.128 in 152,012 control chromosomes in the GnomAD database, including 1,363 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 0.13 (1363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.211 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: 0.128 AC: 19461 AN: 151894 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.128 AC: 19469 AN: 152012 Hom.: 1363 Cov.: 32 AF XY: 0.130 AC XY: 9683 AN XY: 74332

African (AFR) AF: 0.117 AC: 4866 AN: 41434

American (AMR) AF: 0.217 AC: 3313 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.193 AC: 1000 AN: 5178

South Asian (SAS) AF: 0.193 AC: 931 AN: 4820

European-Finnish (FIN) AF: 0.121 AC: 1283 AN: 10570

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7310 AN: 67970

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.0942 Hom.: 267

Bravo AF: 0.136

Asia WGS AF: 0.183 AC: 636 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	1.4
DANN	Benign	0.29
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs13385025; hg19: chr2-62461120;