rs1531590

Positions:

• chr8-75124209-T-C
• chr8-75124209-T-G

Variant summary

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

The ENST00000676364.1(CASC9):​n.251-2453A>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 0.256 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 ENST00000676364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

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 = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375905	XR_929058.3	n.70+1777T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC9	ENST00000676364.1	n.251-2453A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.244

Alfa AF: 0.186 Hom.: 1691

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531590; hg19: chr8-76036444;