rs13282506

Variant names:

• chr8-127446880-G-A
• rs13282506
• ENST00000502056.1:n.1042-3160C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-127446880-G-A
• chr8-127446880-G-C

Variant summary

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

The ENST00000502056.1(CASC8):​n.1042-3160C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,066 control chromosomes in the GnomAD database, including 4,904 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 0.23 (4904 hom., cov: 32)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 7 publications found

Genes affected

CASC8 (HGNC:45129): (cancer susceptibility 8)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC8	NR_024393.1	n.1042-3160C>T		intron_variant	Intron 4 of 4
CASC8	NR_117100.1	n.1042-25917C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC8	ENST00000502056.1	n.1042-3160C>T		intron_variant	Intron 4 of 4	1
CASC8	ENST00000502082.5	n.1042-25917C>T		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34422 AN: 151948 Hom.: 4889 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.227 AC: 34448 AN: 152066 Hom.: 4904 Cov.: 32 AF XY: 0.235 AC XY: 17482 AN XY: 74320

African (AFR) AF: 0.0891 AC: 3696 AN: 41504

American (AMR) AF: 0.341 AC: 5217 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3466

East Asian (EAS) AF: 0.591 AC: 3057 AN: 5170

South Asian (SAS) AF: 0.314 AC: 1508 AN: 4802

European-Finnish (FIN) AF: 0.300 AC: 3166 AN: 10554

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16292 AN: 67976

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.165 Hom.: 566

Bravo AF: 0.222

Asia WGS AF: 0.429 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs13282506; hg19: chr8-128459125;