chr14-54003019-C-T

Variant names:

• chr14-54003019-C-T
• rs4901474

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 0.471 in 152,130 control chromosomes in the GnomAD database, including 18,491 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 0.47 (18491 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 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: 0.472 AC: 71708 AN: 152012 Hom.: 18491 Cov.: 33

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.471 AC: 71723 AN: 152130 Hom.: 18491 Cov.: 33 AF XY: 0.471 AC XY: 34999 AN XY: 74358

African (AFR) AF: 0.253 AC: 10514 AN: 41534

American (AMR) AF: 0.483 AC: 7386 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3470

East Asian (EAS) AF: 0.351 AC: 1814 AN: 5170

South Asian (SAS) AF: 0.460 AC: 2219 AN: 4826

European-Finnish (FIN) AF: 0.572 AC: 6046 AN: 10570

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.588 AC: 39993 AN: 67968

Other (OTH) AF: 0.506 AC: 1066 AN: 2108

Alfa AF: 0.542 Hom.: 70677

Bravo AF: 0.455

Asia WGS AF: 0.436 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4901474; hg19: chr14-54469737;