rs2517452

Variant names:

• chr6-31092385-T-C
• rs2517452

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 0.529 in 152,090 control chromosomes in the GnomAD database, including 21,269 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 0.53 (21269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.581 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: 0.529 AC: 80448 AN: 151972 Hom.: 21254 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.529 AC: 80500 AN: 152090 Hom.: 21269 Cov.: 32 AF XY: 0.528 AC XY: 39217 AN XY: 74344

African (AFR) AF: 0.547 AC: 22683 AN: 41460

American (AMR) AF: 0.522 AC: 7971 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2418 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2451 AN: 5180

South Asian (SAS) AF: 0.599 AC: 2888 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5376 AN: 10568

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34872 AN: 67988

Other (OTH) AF: 0.562 AC: 1189 AN: 2116

Alfa AF: 0.523 Hom.: 20602

Bravo AF: 0.529

Asia WGS AF: 0.532 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.39
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2517452; hg19: chr6-31060162;