4-179202918-C-G

Variant names:

• chr4-179202918-C-G
• rs4862795

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 0.96 in 152,112 control chromosomes in the GnomAD database, including 70,313 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 0.96 (70313 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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: 0.960 AC: 145962 AN: 151994 Hom.: 70273 Cov.: 30

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.953

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.968

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

GnomAD4 genome AF: 0.960 AC: 146061 AN: 152112 Hom.: 70313 Cov.: 30 AF XY: 0.961 AC XY: 71445 AN XY: 74352

African (AFR) AF: 0.878 AC: 36415 AN: 41472

American (AMR) AF: 0.981 AC: 14975 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3415 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5108 AN: 5138

South Asian (SAS) AF: 0.953 AC: 4587 AN: 4812

European-Finnish (FIN) AF: 1.00 AC: 10618 AN: 10622

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67734 AN: 68024

Other (OTH) AF: 0.967 AC: 2043 AN: 2112

Alfa AF: 0.978 Hom.: 8504

Bravo AF: 0.956

Asia WGS AF: 0.943 AC: 3280 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	1.7
DANN	Benign	0.43
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs4862795; hg19: chr4-180124072;