rs10508474

Positions:

• chr10-14489531-T-C

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 0.848 in 152,232 control chromosomes in the GnomAD database, including 54,999 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 0.85 (54999 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.14489531T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129014 AN: 152114 Hom.: 54967 Cov.: 34

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.848 AC: 129104 AN: 152232 Hom.: 54999 Cov.: 34 AF XY: 0.846 AC XY: 62941 AN XY: 74424

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.859

Alfa AF: 0.861 Hom.: 72495

Bravo AF: 0.849

Asia WGS AF: 0.694 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508474; hg19: chr10-14531530;