rs1447295

chr8-127472793-A-Cchr8-127472793-A-Gchr8-127472793-A-T

Variant summary

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

The NR_117100.1(CASC8):n.1041+6290T>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 0.831 in 151,384 control chromosomes in the GnomAD database, including 53,028 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 0.83 (53028 hom., cov: 28)
• Consequence: CASC8 NR_117100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC8	NR_117100.1	n.1041+6290T>G		intron_variant, non_coding_transcript_variant
CASC8	NR_024393.1	n.1041+6290T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC8	ENST00000502056.1	n.1041+6290T>G		intron_variant, non_coding_transcript_variant		1
CASC8	ENST00000502082.5	n.1041+6290T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.831 AC: 125773 AN: 151266 Hom.: 53012 Cov.: 28

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.831 AC: 125832 AN: 151384 Hom.: 53028 Cov.: 28 AF XY: 0.830 AC XY: 61351 AN XY: 73890

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.855

Alfa AF: 0.892 Hom.: 128060

Bravo AF: 0.827

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.51
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1447295; hg19: chr8-128485038;