14-64652958-C-T

Position:

• chr14-64652958-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 0.74 in 152,116 control chromosomes in the GnomAD database, including 41,769 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 0.74 (41769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 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: 0.740 AC: 112411 AN: 151998 Hom.: 41724 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.740 AC: 112507 AN: 152116 Hom.: 41769 Cov.: 32 AF XY: 0.740 AC XY: 54998 AN XY: 74358

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.721

Alfa AF: 0.743 Hom.: 21356

Bravo AF: 0.740

Asia WGS AF: 0.725 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.057
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902304; hg19: chr14-65119676;