8-75235719-T-C

Variant names:

• chr8-75235719-T-C
• rs16939046
• ENST00000504531.3:n.210-11361A>G

Variant summary

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

The ENST00000504531.3(CASC9):​n.210-11361A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 151,948 control chromosomes in the GnomAD database, including 495 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 0.077 (495 hom., cov: 32)
• Consequence: CASC9 ENST00000504531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 11 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504531.3. 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
	CASC9	NR_103848.1		n.230-11361A>G		intron	N/A
	CASC9	NR_103849.2		n.178-11361A>G		intron	N/A
	CASC9	NR_103850.2		n.126-11361A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC9	ENST00000504531.3	TSL:1	n.210-11361A>G		intron	N/A
	CASC9	ENST00000521147.2	TSL:2	n.215-11361A>G		intron	N/A
	CASC9	ENST00000523313.2	TSL:2	n.32+8085A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11648 AN: 151830 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0825

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

GnomAD4 genome AF: 0.0767 AC: 11650 AN: 151948 Hom.: 495 Cov.: 32 AF XY: 0.0773 AC XY: 5742 AN XY: 74294

African (AFR) AF: 0.0453 AC: 1883 AN: 41534

American (AMR) AF: 0.0649 AC: 990 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3462

East Asian (EAS) AF: 0.103 AC: 534 AN: 5182

South Asian (SAS) AF: 0.0619 AC: 299 AN: 4830

European-Finnish (FIN) AF: 0.119 AC: 1265 AN: 10600

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0889 AC: 6026 AN: 67774

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0853 Hom.: 1587

Bravo AF: 0.0710

Asia WGS AF: 0.0850 AC: 296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.91
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16939046; hg19: chr8-76147954;