rs1531590

Variant names:

• chr8-75124209-T-C
• rs1531590
• ENST00000676364.2:n.251-2453A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-75124209-T-C
• chr8-75124209-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.251-2453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,914 control chromosomes in the GnomAD database, including 5,305 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 0.26 (5305 hom., cov: 31)
• Consequence: CASC9 ENST00000676364.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375905	XR_929058.3	n.70+1777T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC9	ENST00000676364.2	n.251-2453A>G		intron_variant	Intron 1 of 2
ENSG00000303615	ENST00000796083.1	n.71+1777T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38881 AN: 151798 Hom.: 5287 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.256 AC: 38942 AN: 151914 Hom.: 5305 Cov.: 31 AF XY: 0.259 AC XY: 19197 AN XY: 74234

African (AFR) AF: 0.355 AC: 14725 AN: 41428

American (AMR) AF: 0.263 AC: 4006 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3464

East Asian (EAS) AF: 0.250 AC: 1281 AN: 5116

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2798 AN: 10566

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13586 AN: 67958

Other (OTH) AF: 0.244 AC: 515 AN: 2108

Alfa AF: 0.215 Hom.: 4693

Bravo AF: 0.261

Asia WGS AF: 0.246 AC: 854 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	1.3
DANN	Benign	0.79
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1531590; hg19: chr8-76036444;