14-64652958-C-T

Variant names:

• chr14-64652958-C-T
• rs4902304

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 0.74 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.731 AC: 30349 AN: 41492

American (AMR) AF: 0.757 AC: 11558 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3490 AN: 5172

South Asian (SAS) AF: 0.752 AC: 3626 AN: 4820

European-Finnish (FIN) AF: 0.747 AC: 7903 AN: 10574

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50518 AN: 67986

Other (OTH) AF: 0.721 AC: 1526 AN: 2116

Alfa AF: 0.743 Hom.: 31755

Bravo AF: 0.740

Asia WGS AF: 0.725 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.057
DANN	Benign	0.36
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs4902304; hg19: chr14-65119676;