15-57918200-G-A

Variant names:

• chr15-57918200-G-A
• rs1530293

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 0.335 in 151,358 control chromosomes in the GnomAD database, including 9,799 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 0.34 (9799 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50707 AN: 151240 Hom.: 9801 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.335 AC: 50711 AN: 151358 Hom.: 9799 Cov.: 31 AF XY: 0.331 AC XY: 24434 AN XY: 73902

African (AFR) AF: 0.181 AC: 7468 AN: 41198

American (AMR) AF: 0.286 AC: 4346 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3468

East Asian (EAS) AF: 0.0867 AC: 437 AN: 5040

South Asian (SAS) AF: 0.137 AC: 651 AN: 4760

European-Finnish (FIN) AF: 0.470 AC: 4928 AN: 10492

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.450 AC: 30524 AN: 67898

Other (OTH) AF: 0.318 AC: 669 AN: 2102

Alfa AF: 0.402 Hom.: 21852

Bravo AF: 0.316

Asia WGS AF: 0.106 AC: 368 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	5.4
DANN	Benign	0.48
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1530293; hg19: chr15-58210398; COSMIC: COSV65731593;