8-127705823-G-T

Position:

• chr8-127705823-G-T

Variant summary

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

The NR_117102.1(CASC11):​n.366-2580C>A 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 0.543 in 152,044 control chromosomes in the GnomAD database, including 23,875 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 0.54 (23875 hom., cov: 32)
• Consequence: CASC11 NR_117102.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

Genes affected

CASC11 (HGNC:48939): (cancer susceptibility 11)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC11	NR_117102.1	n.366-2580C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC11	ENST00000502463.7	n.144-13957C>A		intron_variant, non_coding_transcript_variant		2
CASC11	ENST00000519071.6	n.355-2580C>A		intron_variant, non_coding_transcript_variant		3
CASC11	ENST00000672637.1	n.272-2580C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82481 AN: 151926 Hom.: 23840 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.543 AC: 82571 AN: 152044 Hom.: 23875 Cov.: 32 AF XY: 0.544 AC XY: 40459 AN XY: 74312

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.505

Alfa AF: 0.456 Hom.: 36735

Bravo AF: 0.543

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.94
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9642880; hg19: chr8-128718068;