rs16939046

chr8-75235719-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_103849.2(CASC9):n.178-11361A>G variant causes a intron, non coding transcript 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 NR_103849.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC9	NR_103849.2	n.178-11361A>G		intron_variant, non_coding_transcript_variant
CASC9	NR_103848.1	n.230-11361A>G		intron_variant, non_coding_transcript_variant
CASC9	NR_103850.2	n.126-11361A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC9	ENST00000676364.1	n.250+88502A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0453

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0619

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0875 Hom.: 620

Bravo AF: 0.0710

Asia WGS AF: 0.0850 AC: 296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	3.3
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16939046; hg19: chr8-76147954;