chr14-63552929-C-T

Variant names:

• chr14-63552929-C-T
• rs10498508

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.148 AC: 6130 AN: 41490

American (AMR) AF: 0.0839 AC: 1281 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3470

East Asian (EAS) AF: 0.166 AC: 860 AN: 5180

South Asian (SAS) AF: 0.161 AC: 777 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10576

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6662 AN: 68004

Other (OTH) AF: 0.118 AC: 248 AN: 2108

Alfa AF: 0.106 Hom.: 481

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10498508; hg19: chr14-64019647;