rs10497705

Variant names:

• chr2-189627288-T-C
• rs10497705

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 0.353 in 151,870 control chromosomes in the GnomAD database, including 10,812 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 0.35 (10812 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53603 AN: 151752 Hom.: 10796 Cov.: 30

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.353 AC: 53635 AN: 151870 Hom.: 10812 Cov.: 30 AF XY: 0.366 AC XY: 27147 AN XY: 74210

African (AFR) AF: 0.212 AC: 8772 AN: 41392

American (AMR) AF: 0.492 AC: 7504 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3672 AN: 5160

South Asian (SAS) AF: 0.546 AC: 2630 AN: 4818

European-Finnish (FIN) AF: 0.490 AC: 5154 AN: 10520

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23550 AN: 67948

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.350 Hom.: 32292

Bravo AF: 0.346

Asia WGS AF: 0.594 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.43
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10497705; hg19: chr2-190492014;