14-53966672-A-T

Variant names:

• chr14-53966672-A-T
• rs6572927

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 0.825 in 152,190 control chromosomes in the GnomAD database, including 52,951 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 0.83 (52951 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.826 AC: 125572 AN: 152072 Hom.: 52933 Cov.: 33

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.825 AC: 125629 AN: 152190 Hom.: 52951 Cov.: 33 AF XY: 0.824 AC XY: 61308 AN XY: 74422

African (AFR) AF: 0.655 AC: 27168 AN: 41476

American (AMR) AF: 0.805 AC: 12308 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3266 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3450 AN: 5180

South Asian (SAS) AF: 0.851 AC: 4111 AN: 4830

European-Finnish (FIN) AF: 0.898 AC: 9512 AN: 10596

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62969 AN: 68026

Other (OTH) AF: 0.860 AC: 1818 AN: 2114

Alfa AF: 0.867 Hom.: 7168

Bravo AF: 0.810

Asia WGS AF: 0.775 AC: 2696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs6572927; hg19: chr14-54433390;