4-178960633-T-C

Position:

• chr4-178960633-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.305 in 152,064 control chromosomes in the GnomAD database, including 7,277 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 0.30 (7277 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46288 AN: 151946 Hom.: 7270 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.305 AC: 46328 AN: 152064 Hom.: 7277 Cov.: 31 AF XY: 0.300 AC XY: 22327 AN XY: 74336

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.322

Alfa AF: 0.326 Hom.: 1315

Bravo AF: 0.298

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1075182; hg19: chr4-179881787;