rs649129

Variant names:

• chr9-133278860-T-C
• rs649129

Your query was ambiguous. Multiple possible variants found:

• chr9-133278860-T-C
• chr9-133278860-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.328

Alfa AF: 0.862 Hom.: 2535

Bravo AF: 0.813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.1

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: -;