rs10498281

Variant names:

• chr14-25277153-C-T
• rs10498281

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 0.469 in 151,944 control chromosomes in the GnomAD database, including 16,732 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 0.47 (16732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 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: 0.469 AC: 71191 AN: 151826 Hom.: 16704 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.469 AC: 71263 AN: 151944 Hom.: 16732 Cov.: 32 AF XY: 0.471 AC XY: 35015 AN XY: 74274

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.472

Alfa AF: 0.456 Hom.: 1920

Bravo AF: 0.466

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498281; hg19: chr14-25746359;