rs10497744

Variant names:

• chr2-193626172-G-T
• rs10497744

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.285 in 151,934 control chromosomes in the GnomAD database, including 6,670 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 0.28 (6670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43240 AN: 151814 Hom.: 6662 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.285 AC: 43274 AN: 151934 Hom.: 6670 Cov.: 32 AF XY: 0.290 AC XY: 21538 AN XY: 74244

African (AFR) AF: 0.191 AC: 7913 AN: 41456

American (AMR) AF: 0.415 AC: 6342 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2111 AN: 5150

South Asian (SAS) AF: 0.426 AC: 2054 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2613 AN: 10546

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20583 AN: 67918

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.305 Hom.: 4239

Bravo AF: 0.289

Asia WGS AF: 0.392 AC: 1359 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Benign	0.73
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10497744; hg19: chr2-194490896;