chr16-52552429-A-G

Position:

• chr16-52552429-A-G

Variant summary

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

The NR_033920.1(CASC16):​n.659T>C 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 0.632 in 151,970 control chromosomes in the GnomAD database, including 31,342 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 0.63 (31341 hom., cov: 31)
  • Exomes 𝑓: 0.63 (1 hom.)
• Consequence: CASC16 NR_033920.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC16	NR_033920.1	n.659T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC16	ENST00000510238.8	n.669T>C		non_coding_transcript_exon_variant	4/4	1
CASC16	ENST00000652959.1	n.690T>C		non_coding_transcript_exon_variant	7/7
CASC16	ENST00000565755.1	n.122T>C		non_coding_transcript_exon_variant	2/2	3
CASC16	ENST00000671536.1	n.627T>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96003 AN: 151846 Hom.: 31347 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.625 AC: 5 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.625

GnomAD4 genome AF: 0.632 AC: 96022 AN: 151962 Hom.: 31341 Cov.: 31 AF XY: 0.629 AC XY: 46700 AN XY: 74262

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.637

Alfa AF: 0.702 Hom.: 89100

Bravo AF: 0.617

Asia WGS AF: 0.567 AC: 1972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3803662; hg19: chr16-52586341;