rs8035089

Variant names:

• chr15-89784576-A-G
• rs8035089

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 0.245 in 152,140 control chromosomes in the GnomAD database, including 4,645 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 0.24 (4645 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.293 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: 0.245 AC: 37245 AN: 152020 Hom.: 4648 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.245 AC: 37261 AN: 152140 Hom.: 4645 Cov.: 33 AF XY: 0.238 AC XY: 17722 AN XY: 74384

African (AFR) AF: 0.239 AC: 9916 AN: 41498

American (AMR) AF: 0.213 AC: 3258 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 807 AN: 3472

East Asian (EAS) AF: 0.168 AC: 869 AN: 5170

South Asian (SAS) AF: 0.306 AC: 1474 AN: 4822

European-Finnish (FIN) AF: 0.154 AC: 1634 AN: 10610

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18255 AN: 67974

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.262 Hom.: 8112

Bravo AF: 0.248

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.45
DANN	Benign	0.47
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs8035089; hg19: chr15-90327807; COSMIC: COSV55590245;