15-99757458-A-G

Variant names:

• chr15-99757458-A-G
• rs1993293

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 0.384 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.404

Alfa AF: 0.416 Hom.: 2326

Bravo AF: 0.391

Asia WGS AF: 0.421 AC: 1459 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993293; hg19: chr15-100297663;