9-136928090-C-T

Variant names:

• chr9-136928090-C-T
• rs908831

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 0.633 in 151,884 control chromosomes in the GnomAD database, including 30,665 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 0.63 (30665 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 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: 0.633 AC: 96056 AN: 151766 Hom.: 30653 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.633 AC: 96123 AN: 151884 Hom.: 30665 Cov.: 31 AF XY: 0.637 AC XY: 47318 AN XY: 74250

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.644

Alfa AF: 0.577 Hom.: 4297

Bravo AF: 0.620

Asia WGS AF: 0.766 AC: 2662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs908831; hg19: chr9-139822542;