rs10504591

chr8-75124925-T-Cchr8-75124925-T-G

Variant summary

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

The ENST00000676364.1(CASC9):n.251-3169A>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 0.204 in 152,086 control chromosomes in the GnomAD database, including 3,270 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 0.20 (3270 hom., cov: 32)
• Consequence: CASC9 ENST00000676364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375905	XR_929058.3	n.70+2493T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC9	ENST00000676364.1	n.251-3169A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31074 AN: 151968 Hom.: 3272 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.204 AC: 31075 AN: 152086 Hom.: 3270 Cov.: 32 AF XY: 0.207 AC XY: 15361 AN XY: 74336

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.196

Alfa AF: 0.128 Hom.: 204

Bravo AF: 0.196

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504591; hg19: chr8-76037160;