rs10504592

chr8-75127087-T-C

Variant summary

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

The ENST00000676364.1(CASC9):n.251-5331A>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 0.233 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 ENST00000676364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

Genes affected

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

LOC105375905 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375905	XR_929058.3	n.70+4655T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC9	ENST00000676364.1	n.251-5331A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.222

Alfa AF: 0.218 Hom.: 7607

Bravo AF: 0.229

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504592; hg19: chr8-76039322;