rs10504592

Variant names:

• chr8-75127087-T-C
• rs10504592
• ENST00000676364.2:n.251-5331A>G

Variant summary

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

The ENST00000676364.2(CASC9):​n.251-5331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,026 control chromosomes in the GnomAD database, including 4,268 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 0.23 (4268 hom., cov: 32)
• Consequence: CASC9 ENST00000676364.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 3 publications found

Genes affected

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

ENSG00000303615 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000676364.2. You can select a different transcript below to see updated ACMG assignments.

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
	CASC9	ENST00000676364.2		n.251-5331A>G		intron	N/A
	ENSG00000303615	ENST00000796083.1		n.71+4655T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35356 AN: 151908 Hom.: 4270 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.233 AC: 35361 AN: 152026 Hom.: 4268 Cov.: 32 AF XY: 0.234 AC XY: 17375 AN XY: 74322

African (AFR) AF: 0.279 AC: 11592 AN: 41490

American (AMR) AF: 0.169 AC: 2583 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3472

East Asian (EAS) AF: 0.180 AC: 927 AN: 5162

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4812

European-Finnish (FIN) AF: 0.260 AC: 2756 AN: 10584

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.221 AC: 15036 AN: 67934

Other (OTH) AF: 0.222 AC: 469 AN: 2116

Alfa AF: 0.221 Hom.: 17205

Bravo AF: 0.229

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		0.15

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: rs10504592;

hg19: chr8-76039322;