16-52552429-A-G

Variant names:

• chr16-52552429-A-G
• rs3803662
• ENST00000510238.9:n.676T>C

Variant summary

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

The ENST00000510238.9(CASC16):​n.676T>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 ENST00000510238.9 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 319 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=-0.95).
• 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.659T>C		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.676T>C		non_coding_transcript_exon	Exon 4 of 4
	CASC16	ENST00000565755.2	TSL:3	n.527T>C		non_coding_transcript_exon	Exon 6 of 6
	CASC16	ENST00000652959.1		n.690T>C		non_coding_transcript_exon	Exon 7 of 7

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

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: 0.625 AC: 5 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.482 AC: 19960 AN: 41406

American (AMR) AF: 0.616 AC: 9404 AN: 15274

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

East Asian (EAS) AF: 0.380 AC: 1962 AN: 5160

South Asian (SAS) AF: 0.736 AC: 3529 AN: 4798

European-Finnish (FIN) AF: 0.673 AC: 7120 AN: 10574

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

European-Non Finnish (NFE) AF: 0.732 AC: 49771 AN: 67966

Other (OTH) AF: 0.637 AC: 1343 AN: 2108

Alfa AF: 0.695 Hom.: 181962

Bravo AF: 0.617

Asia WGS AF: 0.567 AC: 1972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.46
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs3803662; hg19: chr16-52586341;