chr4-156672987-C-T

Position:

• chr4-156672987-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 0.174 in 152,046 control chromosomes in the GnomAD database, including 2,746 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 0.17 (2746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.174 AC: 26421 AN: 151928 Hom.: 2733 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.174 AC: 26468 AN: 152046 Hom.: 2746 Cov.: 32 AF XY: 0.174 AC XY: 12934 AN XY: 74338

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.164

Alfa AF: 0.146 Hom.: 1179

Bravo AF: 0.170

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1464452; hg19: chr4-157594139;