ENST00000502056.1:n.1353T>C

Variant names:

• chr8-127443409-A-G
• rs6981397
• ENST00000502056.1:n.1353T>C

Variant summary

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

The ENST00000502056.1(CASC8):​n.1353T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,106 control chromosomes in the GnomAD database, including 7,337 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 0.29 (7337 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CASC8 ENST00000502056.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502056.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	NR_024393.1		n.1353T>C		non_coding_transcript_exon	Exon 5 of 5
	CASC8	NR_117100.1		n.1042-22446T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1353T>C		non_coding_transcript_exon	Exon 5 of 5
	CASC8	ENST00000502082.5	TSL:1	n.1042-22446T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44234 AN: 151988 Hom.: 7324 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.282

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.291 AC: 44263 AN: 152106 Hom.: 7337 Cov.: 32 AF XY: 0.297 AC XY: 22077 AN XY: 74336

African (AFR) AF: 0.150 AC: 6226 AN: 41510

American (AMR) AF: 0.382 AC: 5834 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3472

East Asian (EAS) AF: 0.596 AC: 3089 AN: 5184

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4822

European-Finnish (FIN) AF: 0.365 AC: 3845 AN: 10538

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21651 AN: 67986

Other (OTH) AF: 0.289 AC: 612 AN: 2114

Alfa AF: 0.303 Hom.: 12798

Bravo AF: 0.282

Asia WGS AF: 0.464 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6981397; hg19: chr8-128455654;