9-133278860-T-G

Variant names:

• chr9-133278860-T-G
• rs649129

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.0014 (11 hom., cov: 15)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=2.638).
• BS2: High Homozygotes in GnomAd4 at 11 gene

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: 0.00138 AC: 102 AN: 74114 Hom.: 11 Cov.: 15

Gnomad AFR AF: 0.00167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00145

Gnomad ASJ AF: 0.00108

Gnomad EAS AF: 0.00190

Gnomad SAS AF: 0.00226

Gnomad FIN AF: 0.000966

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00120

Gnomad OTH AF: 0.00198

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

GnomAD4 genome AF: 0.00137 AC: 102 AN: 74196 Hom.: 11 Cov.: 15 AF XY: 0.00139 AC XY: 50 AN XY: 36038

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.00145

Gnomad4 ASJ AF: 0.00108

Gnomad4 EAS AF: 0.00191

Gnomad4 SAS AF: 0.00226

Gnomad4 FIN AF: 0.000966

Gnomad4 NFE AF: 0.00120

Gnomad4 OTH AF: 0.00196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs649129; hg19: -;