rs10496098

chr2-62530324-T-A

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 0.0992 in 152,228 control chromosomes in the GnomAD database, including 891 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 0.099 (891 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0993 AC: 15097 AN: 152110 Hom.: 894 Cov.: 33

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0992 AC: 15097 AN: 152228 Hom.: 891 Cov.: 33 AF XY: 0.0983 AC XY: 7316 AN XY: 74406

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.115

Alfa AF: 0.116 Hom.: 136

Bravo AF: 0.0950

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496098; hg19: chr2-62757459;