rs10148969

Variant names:

• chr14-90502030-C-T
• rs10148969

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 0.416 in 151,802 control chromosomes in the GnomAD database, including 13,742 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 0.42 (13742 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 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: 0.416 AC: 63106 AN: 151686 Hom.: 13737 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.416 AC: 63145 AN: 151802 Hom.: 13742 Cov.: 31 AF XY: 0.425 AC XY: 31547 AN XY: 74178

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.436

Alfa AF: 0.408 Hom.: 6088

Bravo AF: 0.422

Asia WGS AF: 0.591 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10148969; hg19: chr14-90968374;