4-179187526-C-T

Position:

• chr4-179187526-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 0.0692 in 151,958 control chromosomes in the GnomAD database, including 976 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 0.069 (976 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.179187526C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10497 AN: 151844 Hom.: 969 Cov.: 33

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.0321

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0596

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

GnomAD4 genome AF: 0.0692 AC: 10518 AN: 151958 Hom.: 976 Cov.: 33 AF XY: 0.0757 AC XY: 5623 AN XY: 74272

Gnomad4 AFR AF: 0.0344

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.0321

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0599

Alfa AF: 0.0650 Hom.: 165

Bravo AF: 0.0817

Asia WGS AF: 0.256 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520419; hg19: chr4-180108680;