4-156672987-C-T

Variant names:

• chr4-156672987-C-T
• rs1464452

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;