rs10483956

Positions:

• chr14-82484084-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 0.195 in 152,002 control chromosomes in the GnomAD database, including 3,327 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 0.19 (3327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

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 (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29558 AN: 151882 Hom.: 3333 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.195 AC: 29571 AN: 152002 Hom.: 3327 Cov.: 32 AF XY: 0.199 AC XY: 14808 AN XY: 74296

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.201

Alfa AF: 0.190 Hom.: 1446

Bravo AF: 0.194

Asia WGS AF: 0.453 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483956; hg19: chr14-82950428;