rs3803661

Positions:

• chr16-52552565-A-G
• chr16-52552565-A-T

Variant summary

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

The NR_033920.1(CASC16):​n.654-131T>C 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 0.632 in 152,072 control chromosomes in the GnomAD database, including 31,372 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 (31372 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CASC16 NR_033920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

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=-0.94).
• 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.654-131T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC16	ENST00000510238.8	n.664-131T>C		intron_variant, non_coding_transcript_variant		1
CASC16	ENST00000652959.1	n.685-131T>C		intron_variant, non_coding_transcript_variant
CASC16	ENST00000565755.1	n.117-131T>C		intron_variant, non_coding_transcript_variant		3
CASC16	ENST00000671536.1	n.622-131T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96072 AN: 151954 Hom.: 31378 Cov.: 33

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.642

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.632 AC: 96092 AN: 152072 Hom.: 31372 Cov.: 33 AF XY: 0.629 AC XY: 46741 AN XY: 74340

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.638

Alfa AF: 0.697 Hom.: 16079

Bravo AF: 0.617

Asia WGS AF: 0.568 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3803661; hg19: chr16-52586477;