rs16902328

chr8-127701628-T-G

Variant summary

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

The NR_117102.1(CASC11):n.560-789A>C 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 0.0582 in 152,268 control chromosomes in the GnomAD database, including 364 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 0.058 (364 hom., cov: 32)
• Consequence: CASC11 NR_117102.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC11	NR_117102.1	n.560-789A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC11	ENST00000502463.7	n.144-9762A>C		intron_variant, non_coding_transcript_variant		2
CASC11	ENST00000519071.6	n.549-789A>C		intron_variant, non_coding_transcript_variant		3
CASC11	ENST00000672637.1	n.465+1422A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0583 AC: 8867 AN: 152150 Hom.: 368 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0718

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0582 AC: 8858 AN: 152268 Hom.: 364 Cov.: 32 AF XY: 0.0607 AC XY: 4517 AN XY: 74464

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0713

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0714

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0657 Hom.: 525

Bravo AF: 0.0521

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.6
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16902328; hg19: chr8-128713873;