9-133175167-T-C

Position:

• chr9-133175167-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 0.798 in 152,222 control chromosomes in the GnomAD database, including 48,675 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 0.80 (48675 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133175167T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121383 AN: 152104 Hom.: 48631 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.798 AC: 121482 AN: 152222 Hom.: 48675 Cov.: 33 AF XY: 0.802 AC XY: 59709 AN XY: 74432

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.770

Alfa AF: 0.775 Hom.: 6046

Bravo AF: 0.795

Asia WGS AF: 0.781 AC: 2714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7850541; hg19: chr9-136050554;