rs4559029

chr5-121573083-G-Achr5-121573083-G-Cchr5-121573083-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 0.514 in 151,974 control chromosomes in the GnomAD database, including 21,096 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 0.51 (21096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.514 AC: 78060 AN: 151856 Hom.: 21069 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.514 AC: 78112 AN: 151974 Hom.: 21096 Cov.: 32 AF XY: 0.515 AC XY: 38225 AN XY: 74248

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.542

Alfa AF: 0.561 Hom.: 47753

Bravo AF: 0.513

Asia WGS AF: 0.665 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.4
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: rs4559029; hg19: chr5-120908778;