rs9940048

Positions:

• chr16-52629949-G-A

Variant summary

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

The ENST00000652959.1(CASC16):​n.339+1001C>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 0.263 in 151,678 control chromosomes in the GnomAD database, including 5,409 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 0.26 (5409 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: CASC16 ENST00000652959.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

Genes affected

CASC16 (HGNC:48608): (cancer susceptibility 16)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC16	ENST00000652959.1	n.339+1001C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39925 AN: 151556 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.287

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.263 AC: 39944 AN: 151672 Hom.: 5409 Cov.: 32 AF XY: 0.259 AC XY: 19175 AN XY: 74098

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.285

Alfa AF: 0.263 Hom.: 488

Bravo AF: 0.267

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
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: rs9940048; hg19: chr16-52663861;