rs10497652

Variant names:

• chr2-184489318-C-T
• rs10497652

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 0.0859 in 152,166 control chromosomes in the GnomAD database, including 782 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 0.086 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 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: 0.0860 AC: 13072 AN: 152048 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0886

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

GnomAD4 genome AF: 0.0859 AC: 13069 AN: 152166 Hom.: 782 Cov.: 32 AF XY: 0.0849 AC XY: 6313 AN XY: 74390

African (AFR) AF: 0.0236 AC: 981 AN: 41538

American (AMR) AF: 0.0733 AC: 1120 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5176

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4828

European-Finnish (FIN) AF: 0.145 AC: 1530 AN: 10578

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8664 AN: 67992

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.109 Hom.: 1723

Bravo AF: 0.0766

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.40
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10497652; hg19: chr2-185354045;