4-143285795-T-C

Variant names:

• chr4-143285795-T-C
• rs12643013

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 0.472 in 151,964 control chromosomes in the GnomAD database, including 17,816 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 0.47 (17816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.472 AC: 71747 AN: 151846 Hom.: 17810 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.472 AC: 71785 AN: 151964 Hom.: 17816 Cov.: 32 AF XY: 0.478 AC XY: 35531 AN XY: 74264

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.480

Alfa AF: 0.494 Hom.: 37949

Bravo AF: 0.468

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12643013; hg19: chr4-144206948;