rs904208

Variant names:

• chr5-144091362-C-A
• rs904208

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 0.411 in 152,000 control chromosomes in the GnomAD database, including 14,642 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 0.41 (14642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 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: 0.410 AC: 62339 AN: 151880 Hom.: 14595 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.411 AC: 62436 AN: 152000 Hom.: 14642 Cov.: 32 AF XY: 0.408 AC XY: 30350 AN XY: 74304

African (AFR) AF: 0.651 AC: 26986 AN: 41428

American (AMR) AF: 0.332 AC: 5066 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3472

East Asian (EAS) AF: 0.187 AC: 964 AN: 5150

South Asian (SAS) AF: 0.425 AC: 2048 AN: 4816

European-Finnish (FIN) AF: 0.291 AC: 3082 AN: 10574

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21848 AN: 67972

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.357 Hom.: 1831

Bravo AF: 0.421

Asia WGS AF: 0.329 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.48
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs904208; hg19: chr5-143470927;