rs884608

Positions:

• chr9-36500362-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.316

Alfa AF: 0.299 Hom.: 3149

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884608; hg19: chr9-36500359;