14-64652958-C-T

Variant names:

• chr14-64652958-C-T
• rs4902304

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;