chr9-133278860-T-C

Variant names:

• chr9-133278860-T-C
• rs649129

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.32 (7528 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=3.083).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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: 0.325 AC: 26738 AN: 82364 Hom.: 7513 Cov.: 15

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.325 AC: 26777 AN: 82458 Hom.: 7528 Cov.: 15 AF XY: 0.328 AC XY: 13153 AN XY: 40064

African (AFR) AF: 0.375 AC: 7641 AN: 20350

American (AMR) AF: 0.297 AC: 2536 AN: 8526

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 569 AN: 2026

East Asian (EAS) AF: 0.287 AC: 835 AN: 2910

South Asian (SAS) AF: 0.371 AC: 917 AN: 2470

European-Finnish (FIN) AF: 0.315 AC: 1747 AN: 5554

Middle Eastern (MID) AF: 0.277 AC: 52 AN: 188

European-Non Finnish (NFE) AF: 0.309 AC: 11955 AN: 38672

Other (OTH) AF: 0.328 AC: 374 AN: 1140

Alfa AF: 0.861 Hom.: 2821

Bravo AF: 0.813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.1
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; hg19: -;