rs10498065

Variant names:

• chr2-219676450-C-T
• rs10498065

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.084 in 151,732 control chromosomes in the GnomAD database, including 991 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 0.084 (991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 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: 0.0839 AC: 12725 AN: 151620 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0648

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

GnomAD4 genome AF: 0.0840 AC: 12740 AN: 151732 Hom.: 991 Cov.: 32 AF XY: 0.0830 AC XY: 6154 AN XY: 74160

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0436

Gnomad4 ASJ AF: 0.0580

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0562

Gnomad4 FIN AF: 0.0464

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0637

Alfa AF: 0.0617 Hom.: 106

Bravo AF: 0.0882

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498065; hg19: chr2-220541172;