rs2459210

Positions:

• chr10-124455610-A-C
• chr10-124455610-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 0.581 in 151,878 control chromosomes in the GnomAD database, including 26,934 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 0.58 (26934 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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: 0.582 AC: 88261 AN: 151760 Hom.: 26923 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.581 AC: 88303 AN: 151878 Hom.: 26934 Cov.: 31 AF XY: 0.583 AC XY: 43296 AN XY: 74220

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.581

Alfa AF: 0.626 Hom.: 18059

Bravo AF: 0.577

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2459210; hg19: chr10-126144179;