rs10484113

Variant names:

• chr14-85011409-T-C
• rs10484113

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 0.399 in 151,940 control chromosomes in the GnomAD database, including 13,329 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 0.40 (13329 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.545 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: 0.399 AC: 60578 AN: 151820 Hom.: 13318 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.399 AC: 60607 AN: 151940 Hom.: 13329 Cov.: 31 AF XY: 0.399 AC XY: 29618 AN XY: 74260

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.429

Alfa AF: 0.468 Hom.: 18397

Bravo AF: 0.407

Asia WGS AF: 0.345 AC: 1191 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484113; hg19: chr14-85477753;