4-154592124-C-T

Position:

• chr4-154592124-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 0.879 in 152,086 control chromosomes in the GnomAD database, including 58,744 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 0.88 (58744 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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: 0.879 AC: 133595 AN: 151970 Hom.: 58700 Cov.: 30

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.879 AC: 133695 AN: 152086 Hom.: 58744 Cov.: 30 AF XY: 0.878 AC XY: 65251 AN XY: 74328

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.888

Alfa AF: 0.873 Hom.: 10679

Bravo AF: 0.882

Asia WGS AF: 0.891 AC: 3098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070008; hg19: chr4-155513276;