9-133278860-T-G

Variant names:

• chr9-133278860-T-G
• rs649129

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 69 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00166 AC: 30 AN: 18042

American (AMR) AF: 0.00145 AC: 11 AN: 7596

Ashkenazi Jewish (ASJ) AF: 0.00108 AC: 2 AN: 1852

East Asian (EAS) AF: 0.00191 AC: 5 AN: 2618

South Asian (SAS) AF: 0.00226 AC: 5 AN: 2214

European-Finnish (FIN) AF: 0.000966 AC: 5 AN: 5176

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 174

European-Non Finnish (NFE) AF: 0.00120 AC: 42 AN: 34888

Other (OTH) AF: 0.00196 AC: 2 AN: 1022

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 2821

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.6
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs649129;