rs16902364

chr8-127733020-A-C

Variant summary

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

The NR_117102.1(CASC11):n.143+805T>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 0.132 in 152,038 control chromosomes in the GnomAD database, including 2,451 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 0.13 (2451 hom., cov: 32)
• Consequence: CASC11 NR_117102.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944

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 (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC11	NR_117102.1	n.143+805T>G		intron_variant, non_coding_transcript_variant
CASC11	NR_117101.1	n.143+805T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC11	ENST00000502463.7	n.143+805T>G		intron_variant, non_coding_transcript_variant		2
CASC11	ENST00000518376.2	n.141+805T>G		intron_variant, non_coding_transcript_variant		3
CASC11	ENST00000519071.6	n.132+805T>G		intron_variant, non_coding_transcript_variant		3
CASC11	ENST00000672942.1	n.329+805T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20004 AN: 151920 Hom.: 2438 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.132 AC: 20061 AN: 152038 Hom.: 2451 Cov.: 32 AF XY: 0.135 AC XY: 10051 AN XY: 74354

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0873

Alfa AF: 0.0471 Hom.: 504

Bravo AF: 0.135

Asia WGS AF: 0.161 AC: 562 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	1.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16902364; hg19: chr8-128745266; COSMIC: COSV104583426;