rs3112572

Positions:

• chr16-52566535-G-A

Variant summary

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

The NR_033920.1(CASC16):​n.605-3673C>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 0.0846 in 152,016 control chromosomes in the GnomAD database, including 1,083 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 0.085 (1083 hom., cov: 32)
• Consequence: CASC16 NR_033920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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 (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC16	NR_033920.1	n.605-3673C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC16	ENST00000510238.8	n.615-3673C>T		intron_variant, non_coding_transcript_variant		1
CASC16	ENST00000652959.1	n.636-3673C>T		intron_variant, non_coding_transcript_variant
CASC16	ENST00000671536.1	n.622-14101C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12842 AN: 151898 Hom.: 1081 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0527

Gnomad FIN AF: 0.0575

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0740

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0846 AC: 12863 AN: 152016 Hom.: 1083 Cov.: 32 AF XY: 0.0862 AC XY: 6404 AN XY: 74294

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.0496

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.0521

Gnomad4 FIN AF: 0.0575

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0732

Alfa AF: 0.0394 Hom.: 156

Bravo AF: 0.0907

Asia WGS AF: 0.104 AC: 361 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	0.21
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3112572; hg19: chr16-52600447;