14-53964857-C-T

Variant names:

• chr14-53964857-C-T
• rs8014363

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 0.613 in 152,184 control chromosomes in the GnomAD database, including 29,042 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 0.61 (29042 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.612 AC: 93130 AN: 152066 Hom.: 29007 Cov.: 34

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.613 AC: 93224 AN: 152184 Hom.: 29042 Cov.: 34 AF XY: 0.617 AC XY: 45890 AN XY: 74396

African (AFR) AF: 0.659 AC: 27364 AN: 41500

American (AMR) AF: 0.692 AC: 10578 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2137 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4518 AN: 5190

South Asian (SAS) AF: 0.649 AC: 3132 AN: 4828

European-Finnish (FIN) AF: 0.544 AC: 5766 AN: 10594

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37822 AN: 67990

Other (OTH) AF: 0.619 AC: 1309 AN: 2114

Alfa AF: 0.592 Hom.: 13273

Bravo AF: 0.623

Asia WGS AF: 0.767 AC: 2664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.45
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs8014363; hg19: chr14-54431575;