4-178191843-G-C

Variant names:

• chr4-178191843-G-C
• rs722387

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 0.403 in 151,864 control chromosomes in the GnomAD database, including 13,673 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 0.40 (13673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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: 0.404 AC: 61231 AN: 151746 Hom.: 13666 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.403 AC: 61248 AN: 151864 Hom.: 13673 Cov.: 32 AF XY: 0.409 AC XY: 30329 AN XY: 74228

African (AFR) AF: 0.207 AC: 8560 AN: 41440

American (AMR) AF: 0.524 AC: 7998 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1576 AN: 3464

East Asian (EAS) AF: 0.580 AC: 2995 AN: 5166

South Asian (SAS) AF: 0.460 AC: 2211 AN: 4810

European-Finnish (FIN) AF: 0.466 AC: 4895 AN: 10502

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31392 AN: 67918

Other (OTH) AF: 0.448 AC: 946 AN: 2110

Alfa AF: 0.423 Hom.: 1771

Bravo AF: 0.398

Asia WGS AF: 0.529 AC: 1839 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.46
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs722387; hg19: chr4-179112997;