rs10495537

Variant names:

• chr2-6554387-C-T
• rs10495537

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 0.26 in 151,990 control chromosomes in the GnomAD database, including 6,102 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 0.26 (6102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 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: 0.260 AC: 39460 AN: 151872 Hom.: 6096 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.260 AC: 39475 AN: 151990 Hom.: 6102 Cov.: 32 AF XY: 0.264 AC XY: 19622 AN XY: 74258

African (AFR) AF: 0.0869 AC: 3608 AN: 41498

American (AMR) AF: 0.289 AC: 4404 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1095 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2234 AN: 5144

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4824

European-Finnish (FIN) AF: 0.366 AC: 3860 AN: 10540

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21531 AN: 67954

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.298 Hom.: 28711

Bravo AF: 0.244

Asia WGS AF: 0.408 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10495537; hg19: chr2-6694519;