rs16902359

Variant names:

• chr8-127730605-C-T
• rs16902359
• ENST00000518376.2:n.459G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518376.2(CASC11):​n.459G>A variant causes a non coding transcript exon 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 ENST00000518376.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 20 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518376.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	NR_117101.1		n.461G>A		non_coding_transcript_exon	Exon 2 of 2
	CASC11	NR_117102.1		n.143+3220G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	ENST00000518376.2	TSL:3	n.459G>A		non_coding_transcript_exon	Exon 2 of 2
	CASC11	ENST00000672942.2		n.682G>A		non_coding_transcript_exon	Exon 3 of 3
	CASC11	ENST00000774797.1		n.620G>A		non_coding_transcript_exon	Exon 3 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.550 AC: 22759 AN: 41392

American (AMR) AF: 0.207 AC: 3157 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2045 AN: 5174

South Asian (SAS) AF: 0.308 AC: 1481 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2023 AN: 10564

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8122 AN: 68000

Other (OTH) AF: 0.216 AC: 455 AN: 2108

Alfa AF: 0.167 Hom.: 9859

Bravo AF: 0.277

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.66
PhyloP100		0.029

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16902359;

hg19: chr8-128742851;

COSMIC: COSV104583421;