8-75308421-A-G

Variant names:

• chr8-75308421-A-G
• rs1808089
• ENST00000521147.2:n.89+16144T>C

Variant summary

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

The ENST00000521147.2(CASC9):​n.89+16144T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,976 control chromosomes in the GnomAD database, including 18,724 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 0.49 (18724 hom., cov: 32)
• Consequence: CASC9 ENST00000521147.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC9	ENST00000521147.2	TSL:2	n.89+16144T>C		intron	N/A
	CASC9	ENST00000654852.3		n.177+16144T>C		intron	N/A
	CASC9	ENST00000669950.2		n.500+15800T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74582 AN: 151856 Hom.: 18721 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.491 AC: 74607 AN: 151976 Hom.: 18724 Cov.: 32 AF XY: 0.492 AC XY: 36567 AN XY: 74294

African (AFR) AF: 0.399 AC: 16559 AN: 41484

American (AMR) AF: 0.616 AC: 9382 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1886 AN: 5166

South Asian (SAS) AF: 0.522 AC: 2514 AN: 4812

European-Finnish (FIN) AF: 0.519 AC: 5480 AN: 10554

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35363 AN: 67932

Other (OTH) AF: 0.496 AC: 1048 AN: 2112

Alfa AF: 0.514 Hom.: 3875

Bravo AF: 0.497

Asia WGS AF: 0.398 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.29
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1808089; hg19: chr8-76220656;