chr9-133320327-T-G

Position:

• chr9-133320327-T-G

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 0.375 in 151,800 control chromosomes in the GnomAD database, including 12,130 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 0.37 (12130 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133320327T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56786 AN: 151710 Hom.: 12101 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.375 AC: 56867 AN: 151800 Hom.: 12130 Cov.: 32 AF XY: 0.371 AC XY: 27522 AN XY: 74130

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.323

Alfa AF: 0.262 Hom.: 1091

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs493014; hg19: chr9-136187163;