rs7005829

Variant names:

• chr8-127422699-C-T
• rs7005829
• ENST00000502082.5:n.1042-1736G>A

Variant summary

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

The ENST00000502082.5(CASC8):​n.1042-1736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,992 control chromosomes in the GnomAD database, including 5,934 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 0.28 (5934 hom., cov: 32)
• Consequence: CASC8 ENST00000502082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502082.5. 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_117100.1		n.1042-1736G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502082.5	TSL:1	n.1042-1736G>A		intron	N/A
	CASC8	ENST00000842817.1		n.82-1736G>A		intron	N/A
	CASC8	ENST00000842818.1		n.138-1736G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41969 AN: 151874 Hom.: 5936 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.276 AC: 41980 AN: 151992 Hom.: 5934 Cov.: 32 AF XY: 0.278 AC XY: 20613 AN XY: 74260

African (AFR) AF: 0.273 AC: 11309 AN: 41446

American (AMR) AF: 0.216 AC: 3301 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1339 AN: 5178

South Asian (SAS) AF: 0.185 AC: 889 AN: 4816

European-Finnish (FIN) AF: 0.361 AC: 3806 AN: 10532

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18870 AN: 67960

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.255 Hom.: 1413

Bravo AF: 0.267

Asia WGS AF: 0.196 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.26

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: rs7005829;

hg19: chr8-128434944;

COSMIC: COSV71838671;