rs4779584

Variant names:

• chr15-32702555-T-C
• rs4779584

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;