9-133629472-G-T

Position:

• chr9-133629472-G-T

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 0.0797 in 152,182 control chromosomes in the GnomAD database, including 627 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 0.080 (627 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133629472G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000261018	ENST00000564021.1	n.113+3515C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0796 AC: 12101 AN: 152064 Hom.: 625 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0797 AC: 12122 AN: 152182 Hom.: 627 Cov.: 32 AF XY: 0.0797 AC XY: 5928 AN XY: 74404

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0377

Gnomad4 NFE AF: 0.0489

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0543 Hom.: 253

Bravo AF: 0.0847

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3025369; hg19: chr9-136494594;