rs1430579

chr4-140571531-G-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 0.394 in 152,124 control chromosomes in the GnomAD database, including 14,250 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 0.39 (14250 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59844 AN: 152006 Hom.: 14209 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.394 AC: 59941 AN: 152124 Hom.: 14250 Cov.: 33 AF XY: 0.393 AC XY: 29202 AN XY: 74356

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.355

Alfa AF: 0.343 Hom.: 1343

Bravo AF: 0.419

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.6
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1430579; hg19: chr4-141492685;