rs1459543

Variant names:

• chr4-117729190-G-A
• rs1459543

Your query was ambiguous. Multiple possible variants found:

• chr4-117729190-G-A
• chr4-117729190-G-T

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 0.569 in 151,990 control chromosomes in the GnomAD database, including 25,973 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 0.57 (25973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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: 0.569 AC: 86361 AN: 151872 Hom.: 25927 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.569 AC: 86470 AN: 151990 Hom.: 25973 Cov.: 32 AF XY: 0.567 AC XY: 42125 AN XY: 74272

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.586

Alfa AF: 0.443 Hom.: 3074

Bravo AF: 0.593

Asia WGS AF: 0.548 AC: 1902 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	0.67
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1459543; hg19: chr4-118650345;