rs4779584

Positions:

• chr15-32702555-T-C
• chr15-32702555-T-G

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 0.668 in 152,122 control chromosomes in the GnomAD database, including 36,462 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 0.67 (36462 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101515 AN: 152004 Hom.: 36436 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.668 AC: 101591 AN: 152122 Hom.: 36462 Cov.: 33 AF XY: 0.663 AC XY: 49285 AN XY: 74356

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.707

Alfa AF: 0.768 Hom.: 68934

Bravo AF: 0.662

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4779584; hg19: chr15-32994756;