rs4839604

Variant names:

• chr3-143241431-C-T
• rs4839604

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 0.169 in 152,122 control chromosomes in the GnomAD database, including 2,307 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 0.17 (2307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 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: 0.169 AC: 25742 AN: 152004 Hom.: 2307 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.169 AC: 25756 AN: 152122 Hom.: 2307 Cov.: 32 AF XY: 0.169 AC XY: 12563 AN XY: 74384

African (AFR) AF: 0.154 AC: 6397 AN: 41496

American (AMR) AF: 0.176 AC: 2685 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0917 AC: 318 AN: 3468

East Asian (EAS) AF: 0.114 AC: 588 AN: 5180

South Asian (SAS) AF: 0.114 AC: 549 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2349 AN: 10568

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12456 AN: 67978

Other (OTH) AF: 0.155 AC: 328 AN: 2114

Alfa AF: 0.175 Hom.: 4120

Bravo AF: 0.164

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.57
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4839604; hg19: chr3-142960273;