4-147424387-T-C

Variant names:

• chr4-147424387-T-C
• rs1429119

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.572 AC: 23683 AN: 41418

American (AMR) AF: 0.657 AC: 10042 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2229 AN: 3470

East Asian (EAS) AF: 0.695 AC: 3590 AN: 5162

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4820

European-Finnish (FIN) AF: 0.694 AC: 7326 AN: 10550

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44845 AN: 67960

Other (OTH) AF: 0.631 AC: 1332 AN: 2110

Alfa AF: 0.653 Hom.: 4255

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1429119; hg19: chr4-148345539;