rs10498131

Variant names:

• chr2-222191086-G-A
• rs10498131

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 0.302 in 152,116 control chromosomes in the GnomAD database, including 8,702 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 0.30 (8702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.422 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: 0.302 AC: 45889 AN: 151998 Hom.: 8704 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.302 AC: 45887 AN: 152116 Hom.: 8702 Cov.: 32 AF XY: 0.298 AC XY: 22139 AN XY: 74358

African (AFR) AF: 0.112 AC: 4635 AN: 41502

American (AMR) AF: 0.225 AC: 3442 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3472

East Asian (EAS) AF: 0.0905 AC: 469 AN: 5182

South Asian (SAS) AF: 0.197 AC: 948 AN: 4822

European-Finnish (FIN) AF: 0.475 AC: 5017 AN: 10564

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28954 AN: 67978

Other (OTH) AF: 0.297 AC: 627 AN: 2112

Alfa AF: 0.360 Hom.: 1386

Bravo AF: 0.277

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.54
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs10498131; hg19: chr2-223055805;