14-53964782-A-G

Variant names:

• chr14-53964782-A-G
• rs8014071

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 0.312 in 152,186 control chromosomes in the GnomAD database, including 8,664 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 0.31 (8664 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47416 AN: 152068 Hom.: 8665 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.312 AC: 47432 AN: 152186 Hom.: 8664 Cov.: 33 AF XY: 0.314 AC XY: 23357 AN XY: 74384

African (AFR) AF: 0.111 AC: 4622 AN: 41546

American (AMR) AF: 0.364 AC: 5570 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1902 AN: 5180

South Asian (SAS) AF: 0.287 AC: 1386 AN: 4828

European-Finnish (FIN) AF: 0.377 AC: 3983 AN: 10576

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27376 AN: 67978

Other (OTH) AF: 0.359 AC: 759 AN: 2114

Alfa AF: 0.385 Hom.: 14657

Bravo AF: 0.302

Asia WGS AF: 0.334 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.25
DANN	Benign	0.79
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs8014071; hg19: chr14-54431500;