rs10497879

Variant names:

• chr2-204110702-C-T
• rs10497879

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 0.0327 in 152,162 control chromosomes in the GnomAD database, including 117 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 0.033 (117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0579 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: 0.0327 AC: 4979 AN: 152044 Hom.: 115 Cov.: 32

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.00831

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0327 AC: 4981 AN: 152162 Hom.: 117 Cov.: 32 AF XY: 0.0326 AC XY: 2423 AN XY: 74392

African (AFR) AF: 0.0598 AC: 2482 AN: 41492

American (AMR) AF: 0.0328 AC: 502 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3468

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5166

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4824

European-Finnish (FIN) AF: 0.00831 AC: 88 AN: 10588

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1508 AN: 68010

Other (OTH) AF: 0.0336 AC: 71 AN: 2110

Alfa AF: 0.0251 Hom.: 78

Bravo AF: 0.0360

Asia WGS AF: 0.0430 AC: 150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.3
DANN	Benign	0.47
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10497879; hg19: chr2-204975425;