9-133635393-T-C

Variant names:

• chr9-133635393-T-C
• rs1611115

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.796 in 151,818 control chromosomes in the GnomAD database, including 48,324 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.80 (48324 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -3.11
• Publications: 234 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120798 AN: 151700 Hom.: 48284 Cov.: 29

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.796 AC: 120899 AN: 151818 Hom.: 48324 Cov.: 29 AF XY: 0.798 AC XY: 59198 AN XY: 74184

African (AFR) AF: 0.829 AC: 34299 AN: 41388

American (AMR) AF: 0.720 AC: 10981 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2651 AN: 3466

East Asian (EAS) AF: 0.822 AC: 4210 AN: 5120

South Asian (SAS) AF: 0.779 AC: 3736 AN: 4796

European-Finnish (FIN) AF: 0.845 AC: 8901 AN: 10536

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.789 AC: 53650 AN: 67956

Other (OTH) AF: 0.784 AC: 1644 AN: 2098

Alfa AF: 0.782 Hom.: 105605

Bravo AF: 0.788

Asia WGS AF: 0.817 AC: 2841 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	Orthostatic hypotension 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs1611115; hg19: chr9-136500515;