rs4901473

Variant names:

• chr14-53978439-G-A
• rs4901473

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 0.483 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.214 AC: 8879 AN: 41448

American (AMR) AF: 0.492 AC: 7523 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3472

East Asian (EAS) AF: 0.354 AC: 1827 AN: 5168

South Asian (SAS) AF: 0.465 AC: 2241 AN: 4818

European-Finnish (FIN) AF: 0.601 AC: 6335 AN: 10534

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42821 AN: 67964

Other (OTH) AF: 0.508 AC: 1070 AN: 2106

Alfa AF: 0.583 Hom.: 41300

Bravo AF: 0.463

Asia WGS AF: 0.435 AC: 1512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.37
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4901473; hg19: chr14-54445157;