rs2463460

Positions:

• chr2-10524355-G-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 0.185 in 152,146 control chromosomes in the GnomAD database, including 3,402 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 0.18 (3402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.185 AC: 28086 AN: 152028 Hom.: 3394 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.0817

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.185 AC: 28127 AN: 152146 Hom.: 3402 Cov.: 32 AF XY: 0.180 AC XY: 13387 AN XY: 74384

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.0817

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.0874

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.158

Alfa AF: 0.140 Hom.: 974

Bravo AF: 0.194

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2463460; hg19: chr2-10664481;