rs2497306

chr10-92725454-A-Cchr10-92725454-A-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 0.392 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.412

Alfa AF: 0.464 Hom.: 32130

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2497306; hg19: chr10-94485211;