4-179212588-C-T

Position:

• chr4-179212588-C-T

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 0.0901 in 152,114 control chromosomes in the GnomAD database, including 710 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 0.090 (710 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

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 (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13703 AN: 151996 Hom.: 711 Cov.: 33

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0748

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

GnomAD4 genome AF: 0.0901 AC: 13707 AN: 152114 Hom.: 710 Cov.: 33 AF XY: 0.0919 AC XY: 6829 AN XY: 74336

Gnomad4 AFR AF: 0.0723

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.0740

Alfa AF: 0.0836 Hom.: 814

Bravo AF: 0.0923

Asia WGS AF: 0.100 AC: 349 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	0.96
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457402; hg19: chr4-180133742;