16-52552565-A-G

Variant names:

• chr16-52552565-A-G
• rs3803661
• ENST00000510238.9:n.671-131T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510238.9(CASC16):​n.671-131T>C variant causes a intron 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 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• Publications: 9 publications found

Genes affected

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

ENSG00000285800 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510238.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	NR_033920.1		n.654-131T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.671-131T>C		intron	N/A
	CASC16	ENST00000565755.2	TSL:3	n.522-131T>C		intron	N/A
	CASC16	ENST00000652959.1		n.685-131T>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.482 AC: 20000 AN: 41486

American (AMR) AF: 0.616 AC: 9411 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2122 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1960 AN: 5162

South Asian (SAS) AF: 0.735 AC: 3540 AN: 4816

European-Finnish (FIN) AF: 0.673 AC: 7119 AN: 10572

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49786 AN: 67974

Other (OTH) AF: 0.638 AC: 1343 AN: 2106

Alfa AF: 0.697 Hom.: 24568

Bravo AF: 0.617

Asia WGS AF: 0.568 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs3803661; hg19: chr16-52586477;