rs884608

Variant names:

• chr9-36500362-C-T
• rs884608

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 0.294 in 152,166 control chromosomes in the GnomAD database, including 6,808 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 0.29 (6808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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: 0.294 AC: 44706 AN: 152048 Hom.: 6812 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.294 AC: 44701 AN: 152166 Hom.: 6808 Cov.: 32 AF XY: 0.297 AC XY: 22110 AN XY: 74378

African (AFR) AF: 0.239 AC: 9905 AN: 41506

American (AMR) AF: 0.343 AC: 5240 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1174 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2702 AN: 5174

South Asian (SAS) AF: 0.364 AC: 1754 AN: 4822

European-Finnish (FIN) AF: 0.293 AC: 3103 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19917 AN: 68018

Other (OTH) AF: 0.316 AC: 667 AN: 2114

Alfa AF: 0.303 Hom.: 4819

Bravo AF: 0.297

Asia WGS AF: 0.422 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.56
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs884608; hg19: chr9-36500359;