chr15-99757458-A-G

Variant names:

• chr15-99757458-A-G
• rs1993293

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 0.384 in 152,098 control chromosomes in the GnomAD database, including 11,757 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 0.38 (11757 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.486 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: 0.385 AC: 58459 AN: 151980 Hom.: 11755 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.384 AC: 58473 AN: 152098 Hom.: 11757 Cov.: 33 AF XY: 0.387 AC XY: 28779 AN XY: 74352

African (AFR) AF: 0.271 AC: 11228 AN: 41508

American (AMR) AF: 0.495 AC: 7567 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2429 AN: 5174

South Asian (SAS) AF: 0.429 AC: 2074 AN: 4830

European-Finnish (FIN) AF: 0.375 AC: 3951 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28289 AN: 67962

Other (OTH) AF: 0.404 AC: 853 AN: 2114

Alfa AF: 0.411 Hom.: 2339

Bravo AF: 0.391

Asia WGS AF: 0.421 AC: 1459 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.86
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1993293; hg19: chr15-100297663;