14-63552929-C-T

Position:

• chr14-63552929-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.63552929C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;