9-89543310-C-T

Variant names:

• chr9-89543310-C-T
• rs2480490

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 0.364 in 151,862 control chromosomes in the GnomAD database, including 10,127 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 0.36 (10127 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.365 AC: 55315 AN: 151744 Hom.: 10120 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.364 AC: 55344 AN: 151862 Hom.: 10127 Cov.: 31 AF XY: 0.362 AC XY: 26829 AN XY: 74196

African (AFR) AF: 0.382 AC: 15831 AN: 41396

American (AMR) AF: 0.338 AC: 5167 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5164

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4812

European-Finnish (FIN) AF: 0.406 AC: 4276 AN: 10524

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24799 AN: 67916

Other (OTH) AF: 0.380 AC: 801 AN: 2108

Alfa AF: 0.360 Hom.: 32851

Bravo AF: 0.365

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.43
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2480490; hg19: chr9-92158225;