ENST00000521147.2:n.89+16144T>C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC9	ENST00000521147.2	n.89+16144T>C		intron_variant	Intron 1 of 2	2
CASC9	ENST00000654852.2	n.177+16144T>C		intron_variant	Intron 1 of 1
CASC9	ENST00000669950.1	n.472+15800T>C		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.496

Alfa AF: 0.518 Hom.: 3559

Bravo AF: 0.497

Asia WGS AF: 0.398 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1808089; hg19: chr8-76220656;