rs10483634

Positions:

• chr14-54333321-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 0.128 in 152,202 control chromosomes in the GnomAD database, including 1,637 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 0.13 (1637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 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: 0.128 AC: 19448 AN: 152084 Hom.: 1637 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.128 AC: 19445 AN: 152202 Hom.: 1637 Cov.: 32 AF XY: 0.136 AC XY: 10140 AN XY: 74394

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0754

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.126

Alfa AF: 0.155 Hom.: 1196

Bravo AF: 0.120

Asia WGS AF: 0.124 AC: 431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
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: rs10483634; hg19: chr14-54800039;