rs10498065

Positions:

• chr2-219676450-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;