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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000676364.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC9	ENST00000676364.2		n.251-2453A>G		intron	N/A
	ENSG00000303615	ENST00000796083.1		n.71+1777T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1531590;

hg19: chr8-76036444;