chr4-156976632-T-G

Position:

• chr4-156976632-T-G

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 0.137 in 152,150 control chromosomes in the GnomAD database, including 1,574 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 0.14 (1574 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.156976632T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20831 AN: 152032 Hom.: 1572 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.137 AC: 20838 AN: 152150 Hom.: 1574 Cov.: 32 AF XY: 0.139 AC XY: 10367 AN XY: 74416

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0727 Hom.: 91

Bravo AF: 0.135

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13133399; hg19: chr4-157897784;