4-154620137-C-T

Position:

• chr4-154620137-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 0.712 in 151,970 control chromosomes in the GnomAD database, including 39,088 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 0.71 (39088 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108113 AN: 151852 Hom.: 39049 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.712 AC: 108199 AN: 151970 Hom.: 39088 Cov.: 31 AF XY: 0.704 AC XY: 52243 AN XY: 74254

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.701

Alfa AF: 0.696 Hom.: 40624

Bravo AF: 0.719

Asia WGS AF: 0.686 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12648395; hg19: chr4-155541289;