rs2497306

Variant names:

• chr10-92725454-A-C
• rs2497306

Your query was ambiguous. Multiple possible variants found:

• chr10-92725454-A-C
• chr10-92725454-A-G
• chr10-92725454-A-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 0.392 in 151,900 control chromosomes in the GnomAD database, including 13,197 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 0.39 (13197 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.393 AC: 59606 AN: 151782 Hom.: 13199 Cov.: 30

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.392 AC: 59619 AN: 151900 Hom.: 13197 Cov.: 30 AF XY: 0.396 AC XY: 29378 AN XY: 74210

African (AFR) AF: 0.216 AC: 8938 AN: 41462

American (AMR) AF: 0.432 AC: 6591 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3470

East Asian (EAS) AF: 0.136 AC: 704 AN: 5180

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4808

European-Finnish (FIN) AF: 0.543 AC: 5695 AN: 10494

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33484 AN: 67928

Other (OTH) AF: 0.412 AC: 869 AN: 2110

Alfa AF: 0.455 Hom.: 67550

Bravo AF: 0.375

Asia WGS AF: 0.284 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.6
DANN	Benign	0.83
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2497306; hg19: chr10-94485211;