14-65821192-C-T

Variant names:

• chr14-65821192-C-T
• rs7494064

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 0.898 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.904 AC: 37549 AN: 41534

American (AMR) AF: 0.922 AC: 14117 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2775 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4934 AN: 5176

South Asian (SAS) AF: 0.930 AC: 4492 AN: 4832

European-Finnish (FIN) AF: 0.902 AC: 9567 AN: 10612

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60469 AN: 68012

Other (OTH) AF: 0.902 AC: 1906 AN: 2112

Alfa AF: 0.891 Hom.: 124411

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
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs7494064; hg19: chr14-66287910;