rs615599

Variant names:

• chr5-76797333-C-G
• rs615599

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.407 AC: 16878 AN: 41468

American (AMR) AF: 0.487 AC: 7422 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1859 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2101 AN: 5158

South Asian (SAS) AF: 0.486 AC: 2344 AN: 4822

European-Finnish (FIN) AF: 0.385 AC: 4068 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25960 AN: 67968

Other (OTH) AF: 0.406 AC: 858 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs615599; hg19: chr5-76093158;