8-127470851-G-A

Variant names:

• chr8-127470851-G-A
• rs6981424
• ENST00000502056.1:n.1041+8232C>T

Variant summary

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

The ENST00000502056.1(CASC8):​n.1041+8232C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,902 control chromosomes in the GnomAD database, including 8,320 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 0.31 (8320 hom., cov: 32)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	NR_024393.1		n.1041+8232C>T		intron	N/A
	CASC8	NR_117100.1		n.1041+8232C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1041+8232C>T		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+8232C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46632 AN: 151784 Hom.: 8319 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.307 AC: 46633 AN: 151902 Hom.: 8320 Cov.: 32 AF XY: 0.305 AC XY: 22601 AN XY: 74210

African (AFR) AF: 0.128 AC: 5322 AN: 41436

American (AMR) AF: 0.284 AC: 4336 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3464

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5172

South Asian (SAS) AF: 0.414 AC: 1984 AN: 4796

European-Finnish (FIN) AF: 0.319 AC: 3356 AN: 10518

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28074 AN: 67960

Other (OTH) AF: 0.322 AC: 678 AN: 2106

Alfa AF: 0.370 Hom.: 32846

Bravo AF: 0.292

Asia WGS AF: 0.282 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-0.23

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: rs6981424;

hg19: chr8-128483096;