rs3112612

chr16-52601252-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.472+5252C>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 0.449 in 151,978 control chromosomes in the GnomAD database, including 15,843 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 0.45 (15843 hom., cov: 32)
• Consequence: CASC16 NR_033920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC16	NR_033920.1	n.472+5252C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC16	ENST00000510238.8	n.482+5252C>T		intron_variant, non_coding_transcript_variant		1
CASC16	ENST00000652959.1	n.340-10185C>T		intron_variant, non_coding_transcript_variant
CASC16	ENST00000563844.1	n.313-10185C>T		intron_variant, non_coding_transcript_variant		3
CASC16	ENST00000671536.1	n.489+5252C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68111 AN: 151860 Hom.: 15823 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.449 AC: 68178 AN: 151978 Hom.: 15843 Cov.: 32 AF XY: 0.448 AC XY: 33260 AN XY: 74288

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.505

Alfa AF: 0.445 Hom.: 35801

Bravo AF: 0.462

Asia WGS AF: 0.576 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3112612; hg19: chr16-52635164;