rs580839

Variant names:

• chr15-34706628-G-A
• rs580839

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 0.499 in 151,958 control chromosomes in the GnomAD database, including 19,992 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 0.50 (19992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.499 AC: 75696 AN: 151840 Hom.: 19955 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.499 AC: 75789 AN: 151958 Hom.: 19992 Cov.: 32 AF XY: 0.493 AC XY: 36627 AN XY: 74252

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.468

Alfa AF: 0.461 Hom.: 3364

Bravo AF: 0.507

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
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: rs580839; hg19: chr15-34998829;