rs615599

Positions:

• chr5-76797333-C-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 0.408 in 152,026 control chromosomes in the GnomAD database, including 12,822 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 0.41 (12822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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 (AMR) allele frequency at 95% confidence interval = 0.477 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: 0.408 AC: 62051 AN: 151908 Hom.: 12813 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.408 AC: 62086 AN: 152026 Hom.: 12822 Cov.: 32 AF XY: 0.412 AC XY: 30596 AN XY: 74286

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.406

Alfa AF: 0.387 Hom.: 1413

Bravo AF: 0.417

Asia WGS AF: 0.458 AC: 1593 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	2.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs615599; hg19: chr5-76093158;