ENST00000521147.2:n.89+6499C>A

Variant names:

• chr8-75318066-G-T
• rs6472903
• ENST00000521147.2:n.89+6499C>A

Variant summary

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

The ENST00000521147.2(CASC9):​n.89+6499C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,136 control chromosomes in the GnomAD database, including 56,526 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 0.86 (56526 hom., cov: 33)
• Consequence: CASC9 ENST00000521147.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 65 publications found

Genes affected

CASC9 (HGNC:48906): (cancer susceptibility 9)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521147.2. You can select a different transcript below to see updated ACMG assignments.

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
	CASC9	ENST00000521147.2	TSL:2	n.89+6499C>A		intron	N/A
	CASC9	ENST00000654852.3		n.177+6499C>A		intron	N/A
	CASC9	ENST00000669950.2		n.500+6155C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130937 AN: 152018 Hom.: 56471 Cov.: 33

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.861 AC: 131053 AN: 152136 Hom.: 56526 Cov.: 33 AF XY: 0.865 AC XY: 64300 AN XY: 74374

African (AFR) AF: 0.900 AC: 37401 AN: 41534

American (AMR) AF: 0.896 AC: 13691 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2879 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4996 AN: 5184

South Asian (SAS) AF: 0.898 AC: 4334 AN: 4826

European-Finnish (FIN) AF: 0.809 AC: 8567 AN: 10592

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56353 AN: 67942

Other (OTH) AF: 0.876 AC: 1846 AN: 2108

Alfa AF: 0.844 Hom.: 168315

Bravo AF: 0.869

Asia WGS AF: 0.939 AC: 3265 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.38
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs6472903; hg19: chr8-76230301;