chr4-178480279-G-A

Variant names:

• chr4-178480279-G-A
• rs2702449

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 0.341 in 151,822 control chromosomes in the GnomAD database, including 8,853 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 0.34 (8853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.341 AC: 51696 AN: 151704 Hom.: 8854 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.341 AC: 51714 AN: 151822 Hom.: 8853 Cov.: 32 AF XY: 0.339 AC XY: 25181 AN XY: 74188

African (AFR) AF: 0.304 AC: 12604 AN: 41418

American (AMR) AF: 0.319 AC: 4851 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2322 AN: 5156

South Asian (SAS) AF: 0.439 AC: 2110 AN: 4810

European-Finnish (FIN) AF: 0.322 AC: 3394 AN: 10550

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24004 AN: 67874

Other (OTH) AF: 0.355 AC: 749 AN: 2108

Alfa AF: 0.341 Hom.: 10442

Bravo AF: 0.339

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.71
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2702449; hg19: chr4-179401433;