chr14-63552929-C-T

Variant names:

• chr14-63552929-C-T
• rs10498508

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 0.117 in 152,120 control chromosomes in the GnomAD database, including 1,107 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 0.12 (1107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 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: 0.117 AC: 17709 AN: 152002 Hom.: 1102 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.117 AC: 17738 AN: 152120 Hom.: 1107 Cov.: 32 AF XY: 0.118 AC XY: 8807 AN XY: 74352

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0839

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0980

Gnomad4 OTH AF: 0.118

Alfa AF: 0.106 Hom.: 425

Bravo AF: 0.113

Asia WGS AF: 0.180 AC: 623 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.8
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: rs10498508; hg19: chr14-64019647;