rs115849089

Variant names:

• chr8-20054859-G-A
• rs115849089

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 0.0993 in 152,238 control chromosomes in the GnomAD database, including 840 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 0.099 (840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 32 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 (SAS) allele frequency at 95% confidence interval = 0.127 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: 0.0994 AC: 15120 AN: 152120 Hom.: 840 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.0824

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0993 AC: 15117 AN: 152238 Hom.: 840 Cov.: 32 AF XY: 0.0993 AC XY: 7389 AN XY: 74438

African (AFR) AF: 0.0584 AC: 2426 AN: 41558

American (AMR) AF: 0.0824 AC: 1261 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 633 AN: 3468

East Asian (EAS) AF: 0.118 AC: 611 AN: 5158

South Asian (SAS) AF: 0.136 AC: 655 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1213 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7862 AN: 67994

Other (OTH) AF: 0.103 AC: 218 AN: 2112

Alfa AF: 0.0574 Hom.: 98

Bravo AF: 0.0943

Asia WGS AF: 0.126 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs115849089; hg19: chr8-19912370;