rs10496802

Variant names:

• chr2-138887302-C-A
• rs10496802

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 0.159 in 152,070 control chromosomes in the GnomAD database, including 2,065 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 0.16 (2065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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: 0.159 AC: 24183 AN: 151952 Hom.: 2065 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.159 AC: 24185 AN: 152070 Hom.: 2065 Cov.: 32 AF XY: 0.156 AC XY: 11630 AN XY: 74332

African (AFR) AF: 0.117 AC: 4865 AN: 41488

American (AMR) AF: 0.118 AC: 1806 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3468

East Asian (EAS) AF: 0.0584 AC: 301 AN: 5154

South Asian (SAS) AF: 0.205 AC: 986 AN: 4806

European-Finnish (FIN) AF: 0.195 AC: 2058 AN: 10568

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13019 AN: 67982

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.182 Hom.: 1508

Bravo AF: 0.150

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.67
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10496802; hg19: chr2-139644872;