rs10498091

Positions:

• chr2-221034724-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 0.174 in 152,140 control chromosomes in the GnomAD database, including 2,563 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 0.17 (2563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 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: 0.174 AC: 26475 AN: 152022 Hom.: 2561 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.174 AC: 26508 AN: 152140 Hom.: 2563 Cov.: 32 AF XY: 0.171 AC XY: 12692 AN XY: 74386

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.167

Alfa AF: 0.156 Hom.: 3874

Bravo AF: 0.180

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498091; hg19: chr2-221899444;