rs649129

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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: -;