rs906892

Variant names:

• chr8-599908-A-G
• rs906892

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 0.178 in 152,186 control chromosomes in the GnomAD database, including 2,635 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 0.18 (2635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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: 0.178 AC: 27031 AN: 152068 Hom.: 2628 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.178 AC: 27049 AN: 152186 Hom.: 2635 Cov.: 32 AF XY: 0.184 AC XY: 13687 AN XY: 74388

African (AFR) AF: 0.167 AC: 6926 AN: 41532

American (AMR) AF: 0.276 AC: 4217 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 720 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1575 AN: 5172

South Asian (SAS) AF: 0.278 AC: 1337 AN: 4806

European-Finnish (FIN) AF: 0.172 AC: 1819 AN: 10594

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 9990 AN: 68016

Other (OTH) AF: 0.155 AC: 328 AN: 2116

Alfa AF: 0.163 Hom.: 2906

Bravo AF: 0.184

Asia WGS AF: 0.293 AC: 1019 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	0.091
DANN	Benign	0.27
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs906892; hg19: chr8-549908;