rs10504591

Variant names:

• chr8-75124925-T-C
• rs10504591
• ENST00000676364.2:n.251-3169A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-75124925-T-C
• chr8-75124925-T-G

Variant summary

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

The ENST00000676364.2(CASC9):​n.251-3169A>G variant causes a intron 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 ENST00000676364.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 2 publications found

Genes affected

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

ENSG00000303615 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375905	XR_929058.3	n.70+2493T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC9	ENST00000676364.2	n.251-3169A>G		intron_variant	Intron 1 of 2
ENSG00000303615	ENST00000796083.1	n.71+2493T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.184 AC: 7647 AN: 41484

American (AMR) AF: 0.159 AC: 2424 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 581 AN: 3468

East Asian (EAS) AF: 0.179 AC: 927 AN: 5168

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4820

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10582

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14929 AN: 67982

Other (OTH) AF: 0.196 AC: 415 AN: 2114

Alfa AF: 0.131 Hom.: 216

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10504591; hg19: chr8-76037160;