chr4-156558922-C-T

Position:

• chr4-156558922-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 0.593 in 151,982 control chromosomes in the GnomAD database, including 27,409 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 0.59 (27409 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.156558922C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90021 AN: 151862 Hom.: 27382 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.593 AC: 90102 AN: 151982 Hom.: 27409 Cov.: 32 AF XY: 0.588 AC XY: 43687 AN XY: 74300

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.582

Alfa AF: 0.615 Hom.: 24396

Bravo AF: 0.583

Asia WGS AF: 0.368 AC: 1285 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	0.93
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2090870; hg19: chr4-157480074;