rs4901473

Variant names:

• chr14-53978439-G-A
• rs4901473

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.483 in 151,998 control chromosomes in the GnomAD database, including 20,115 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 0.48 (20115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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: 0.483 AC: 73429 AN: 151884 Hom.: 20119 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.483 AC: 73428 AN: 151998 Hom.: 20115 Cov.: 32 AF XY: 0.482 AC XY: 35815 AN XY: 74282

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.508

Alfa AF: 0.596 Hom.: 28765

Bravo AF: 0.463

Asia WGS AF: 0.435 AC: 1512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4901473; hg19: chr14-54445157;