4-147424387-T-C

Position:

• chr4-147424387-T-C

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 0.635 in 151,978 control chromosomes in the GnomAD database, including 30,932 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 0.63 (30932 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.635 AC: 96397 AN: 151860 Hom.: 30909 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.635 AC: 96457 AN: 151978 Hom.: 30932 Cov.: 31 AF XY: 0.636 AC XY: 47236 AN XY: 74270

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.631

Alfa AF: 0.657 Hom.: 4138

Bravo AF: 0.631

Asia WGS AF: 0.578 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1429119; hg19: chr4-148345539;