rs10496982

Variant names:

• chr2-145550546-A-C
• rs10496982

Your query was ambiguous. Multiple possible variants found:

• chr2-145550546-A-C
• chr2-145550546-A-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 0.14 in 151,798 control chromosomes in the GnomAD database, including 2,273 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 0.14 (2273 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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: 0.140 AC: 21273 AN: 151680 Hom.: 2270 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.140 AC: 21299 AN: 151798 Hom.: 2273 Cov.: 31 AF XY: 0.141 AC XY: 10490 AN XY: 74196

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0907 Hom.: 1093

Bravo AF: 0.148

Asia WGS AF: 0.188 AC: 651 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496982; hg19: chr2-146308114;