9-133276029-C-A

Position:

• chr9-133276029-C-A

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 0.252 in 152,080 control chromosomes in the GnomAD database, including 5,079 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 0.25 (5079 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

(HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133276029C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000651471.1	n.-5G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38360 AN: 151962 Hom.: 5075 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.252 AC: 38378 AN: 152080 Hom.: 5079 Cov.: 33 AF XY: 0.253 AC XY: 18797 AN XY: 74334

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.246

Alfa AF: 0.238 Hom.: 5940

Bravo AF: 0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs568203; hg19: chr9-136151445;