rs1430579

Variant names:

• chr4-140571531-G-C
• rs1430579

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 0.394 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.664 AC: 27554 AN: 41478

American (AMR) AF: 0.405 AC: 6187 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2522 AN: 5182

South Asian (SAS) AF: 0.372 AC: 1795 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2295 AN: 10588

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17262 AN: 67994

Other (OTH) AF: 0.355 AC: 750 AN: 2112

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
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1430579; hg19: chr4-141492685;