15-99759034-G-A

Variant names:

• chr15-99759034-G-A
• rs6598266

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 0.194 in 151,928 control chromosomes in the GnomAD database, including 3,593 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 0.19 (3593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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: 0.194 AC: 29502 AN: 151810 Hom.: 3588 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.194 AC: 29537 AN: 151928 Hom.: 3593 Cov.: 32 AF XY: 0.188 AC XY: 13954 AN XY: 74242

African (AFR) AF: 0.341 AC: 14098 AN: 41388

American (AMR) AF: 0.143 AC: 2187 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3470

East Asian (EAS) AF: 0.0625 AC: 323 AN: 5172

South Asian (SAS) AF: 0.136 AC: 655 AN: 4810

European-Finnish (FIN) AF: 0.0958 AC: 1011 AN: 10558

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10427 AN: 67956

Other (OTH) AF: 0.175 AC: 370 AN: 2110

Alfa AF: 0.170 Hom.: 516

Bravo AF: 0.203

Asia WGS AF: 0.114 AC: 397 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.52
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6598266; hg19: chr15-100299239;