rs16902359

chr8-127730605-C-T

Variant summary

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

The NR_117102.1(CASC11):n.143+3220G>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 0.268 in 152,002 control chromosomes in the GnomAD database, including 8,134 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 0.27 (8134 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: CASC11 NR_117102.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC11	NR_117102.1	n.143+3220G>A		intron_variant, non_coding_transcript_variant
CASC11	NR_117101.1	n.461G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC11	ENST00000502463.7	n.143+3220G>A		intron_variant, non_coding_transcript_variant		2
CASC11	ENST00000518376.2	n.459G>A		non_coding_transcript_exon_variant	2/2	3
CASC11	ENST00000672942.1	n.647G>A		non_coding_transcript_exon_variant	3/3
CASC11	ENST00000519071.6	n.132+3220G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40640 AN: 151876 Hom.: 8100 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.268 AC: 40723 AN: 151994 Hom.: 8134 Cov.: 32 AF XY: 0.273 AC XY: 20261 AN XY: 74292

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.216

Alfa AF: 0.142 Hom.: 2417

Bravo AF: 0.277

Asia WGS AF: 0.330 AC: 1149 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	3.3
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16902359; hg19: chr8-128742851; COSMIC: COSV104583421;