4-178048839-G-A

Variant names:

• chr4-178048839-G-A
• rs966108

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 0.188 in 151,958 control chromosomes in the GnomAD database, including 3,194 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 0.19 (3194 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 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: 0.188 AC: 28610 AN: 151838 Hom.: 3195 Cov.: 31

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.188 AC: 28609 AN: 151958 Hom.: 3194 Cov.: 31 AF XY: 0.190 AC XY: 14136 AN XY: 74252

African (AFR) AF: 0.0610 AC: 2527 AN: 41398

American (AMR) AF: 0.170 AC: 2596 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5166

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4812

European-Finnish (FIN) AF: 0.269 AC: 2840 AN: 10552

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16936 AN: 67956

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.221 Hom.: 1568

Bravo AF: 0.173

Asia WGS AF: 0.214 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs966108; hg19: chr4-178969993;