9-25192575-C-T

Variant names:

• chr9-25192575-C-T
• rs181881383

Variant summary

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

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 0.084 (285 hom., cov: 17)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 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: 0.0845 AC: 7429 AN: 87918 Hom.: 285 Cov.: 17

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0467

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0844 AC: 7422 AN: 87934 Hom.: 285 Cov.: 17 AF XY: 0.0841 AC XY: 3517 AN XY: 41836

African (AFR) AF: 0.0506 AC: 833 AN: 16466

American (AMR) AF: 0.0786 AC: 693 AN: 8814

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 319 AN: 2574

East Asian (EAS) AF: 0.125 AC: 454 AN: 3640

South Asian (SAS) AF: 0.139 AC: 359 AN: 2584

European-Finnish (FIN) AF: 0.0467 AC: 201 AN: 4308

Middle Eastern (MID) AF: 0.0968 AC: 18 AN: 186

European-Non Finnish (NFE) AF: 0.0930 AC: 4435 AN: 47704

Other (OTH) AF: 0.0894 AC: 93 AN: 1040

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	8.8
DANN	Benign	0.90
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs181881383; hg19: chr9-25192573; COSMIC: COSV55710415;