rs1429142

Variant names:

• chr4-147368237-T-C
• rs1429142

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 0.335 in 152,124 control chromosomes in the GnomAD database, including 12,653 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 0.33 (12653 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 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: 0.335 AC: 50858 AN: 152004 Hom.: 12620 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.335 AC: 50945 AN: 152124 Hom.: 12653 Cov.: 32 AF XY: 0.333 AC XY: 24751 AN XY: 74414

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.310

Alfa AF: 0.193 Hom.: 7361

Bravo AF: 0.357

Asia WGS AF: 0.403 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1429142; hg19: chr4-148289389;