14-65821192-C-T

Variant names:

• chr14-65821192-C-T
• rs7494064

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 0.898 in 152,262 control chromosomes in the GnomAD database, including 61,441 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 0.90 (61441 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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: 0.898 AC: 136637 AN: 152144 Hom.: 61390 Cov.: 34

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.898 AC: 136746 AN: 152262 Hom.: 61441 Cov.: 34 AF XY: 0.900 AC XY: 66991 AN XY: 74458

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.902

Alfa AF: 0.887 Hom.: 78105

Bravo AF: 0.898

Asia WGS AF: 0.922 AC: 3207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7494064; hg19: chr14-66287910;