rs1989787

Variant names:

• chr9-133634290-C-T
• rs1989787

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 0.238 in 152,228 control chromosomes in the GnomAD database, including 5,196 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 0.24 (5196 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36271 AN: 152110 Hom.: 5196 Cov.: 34

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.238 AC: 36274 AN: 152228 Hom.: 5196 Cov.: 34 AF XY: 0.233 AC XY: 17351 AN XY: 74440

African (AFR) AF: 0.104 AC: 4326 AN: 41546

American (AMR) AF: 0.222 AC: 3398 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5182

South Asian (SAS) AF: 0.128 AC: 616 AN: 4828

European-Finnish (FIN) AF: 0.309 AC: 3275 AN: 10592

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22992 AN: 67996

Other (OTH) AF: 0.241 AC: 509 AN: 2114

Alfa AF: 0.263 Hom.: 861

Bravo AF: 0.227

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.79
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1989787; hg19: chr9-136499412;