4-178478369-G-A

Variant names:

• chr4-178478369-G-A
• rs2702414

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 0.115 in 151,980 control chromosomes in the GnomAD database, including 1,760 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 0.12 (1760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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: 0.115 AC: 17466 AN: 151862 Hom.: 1743 Cov.: 32

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0809

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.115 AC: 17498 AN: 151980 Hom.: 1760 Cov.: 32 AF XY: 0.122 AC XY: 9046 AN XY: 74296

African (AFR) AF: 0.0640 AC: 2655 AN: 41502

American (AMR) AF: 0.301 AC: 4587 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0900 AC: 312 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2166 AN: 5148

South Asian (SAS) AF: 0.155 AC: 747 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1135 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0809 AC: 5494 AN: 67924

Other (OTH) AF: 0.142 AC: 299 AN: 2108

Alfa AF: 0.102 Hom.: 5877

Bravo AF: 0.131

Asia WGS AF: 0.230 AC: 797 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.52
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2702414; hg19: chr4-179399523; COSMIC: COSV68635165;