9-121798574-C-T

Variant names:

• chr9-121798574-C-T
• rs10818593

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 0.223 in 147,306 control chromosomes in the GnomAD database, including 3,802 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 0.22 (3802 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 32806 AN: 147200 Hom.: 3792 Cov.: 28

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.223 AC: 32825 AN: 147306 Hom.: 3802 Cov.: 28 AF XY: 0.227 AC XY: 16196 AN XY: 71316

African (AFR) AF: 0.158 AC: 6257 AN: 39628

American (AMR) AF: 0.210 AC: 3011 AN: 14338

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 622 AN: 3440

East Asian (EAS) AF: 0.354 AC: 1753 AN: 4950

South Asian (SAS) AF: 0.311 AC: 1444 AN: 4648

European-Finnish (FIN) AF: 0.283 AC: 2736 AN: 9672

Middle Eastern (MID) AF: 0.182 AC: 50 AN: 274

European-Non Finnish (NFE) AF: 0.241 AC: 16242 AN: 67412

Other (OTH) AF: 0.206 AC: 422 AN: 2050

Alfa AF: 0.234 Hom.: 17421

Bravo AF: 0.211

Asia WGS AF: 0.318 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.42
DANN	Benign	0.81
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10818593;

hg19: chr9-124560853;