15-57788419-G-A

Variant names:

• chr15-57788419-G-A
• rs1559777

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 0.279 in 151,876 control chromosomes in the GnomAD database, including 6,575 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 0.28 (6575 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 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: 0.279 AC: 42309 AN: 151756 Hom.: 6550 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.279 AC: 42390 AN: 151876 Hom.: 6575 Cov.: 31 AF XY: 0.280 AC XY: 20818 AN XY: 74246

African (AFR) AF: 0.423 AC: 17522 AN: 41380

American (AMR) AF: 0.234 AC: 3573 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3464

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5168

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4808

European-Finnish (FIN) AF: 0.241 AC: 2542 AN: 10548

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15235 AN: 67922

Other (OTH) AF: 0.253 AC: 535 AN: 2114

Alfa AF: 0.264 Hom.: 4978

Bravo AF: 0.284

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.55
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1559777; hg19: chr15-58080617;