rs4904864

Variant names:

• chr14-92298175-A-G
• rs4904864

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 0.551 in 151,930 control chromosomes in the GnomAD database, including 23,937 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 0.55 (23937 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -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 = 0.64 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: 0.551 AC: 83721 AN: 151814 Hom.: 23928 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.551 AC: 83767 AN: 151930 Hom.: 23937 Cov.: 31 AF XY: 0.545 AC XY: 40474 AN XY: 74238

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.526

Alfa AF: 0.605 Hom.: 14094

Bravo AF: 0.534

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4904864; hg19: chr14-92764519;