9-133279427-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.832 in 152,122 control chromosomes in the GnomAD database, including 52,890 homozygotes. 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 0.83 (52890 hom., cov: 31)
• 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 (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.832 AC: 126436 AN: 152004 Hom.: 52823 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.832 AC: 126562 AN: 152122 Hom.: 52890 Cov.: 31 AF XY: 0.834 AC XY: 62001 AN XY: 74338

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.826

Alfa AF: 0.833 Hom.: 4633

Bravo AF: 0.837

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.5

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs635634; hg19: chr9-136155000;