rs12547643

chr8-127700928-G-A

Variant summary

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

The NR_117102.1(CASC11):n.560-89C>T 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 152,052 control chromosomes in the GnomAD database, including 6,359 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 (6359 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: CASC11 NR_117102.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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 (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC11	NR_117102.1	n.560-89C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC11	ENST00000502463.7	n.144-9062C>T		intron_variant, non_coding_transcript_variant		2
CASC11	ENST00000519071.6	n.549-89C>T		intron_variant, non_coding_transcript_variant		3
CASC11	ENST00000672637.1	n.466-1369C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40658 AN: 151930 Hom.: 6347 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.274

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

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.268 AC: 40691 AN: 152048 Hom.: 6359 Cov.: 32 AF XY: 0.271 AC XY: 20121 AN XY: 74312

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.283

Alfa AF: 0.330 Hom.: 12297

Bravo AF: 0.242

Asia WGS AF: 0.282 AC: 984 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	0.23
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12547643; hg19: chr8-128713173;