chr16-52591640-A-G

Variant names:

• chr16-52591640-A-G
• rs3112625
• ENST00000510238.9:n.490-573T>C

Variant summary

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

The ENST00000510238.9(CASC16):​n.490-573T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,926 control chromosomes in the GnomAD database, including 17,986 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 0.48 (17986 hom., cov: 32)
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 10 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC16	NR_033920.1	n.473-573T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC16	ENST00000510238.9	n.490-573T>C		intron_variant	Intron 1 of 3	1
CASC16	ENST00000826549.1	n.358T>C		non_coding_transcript_exon_variant	Exon 1 of 4
CASC16	ENST00000826550.1	n.291T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72524 AN: 151808 Hom.: 17949 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.478 AC: 72616 AN: 151926 Hom.: 17986 Cov.: 32 AF XY: 0.475 AC XY: 35282 AN XY: 74224

African (AFR) AF: 0.528 AC: 21881 AN: 41428

American (AMR) AF: 0.552 AC: 8418 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1833 AN: 3468

East Asian (EAS) AF: 0.784 AC: 4029 AN: 5138

South Asian (SAS) AF: 0.459 AC: 2207 AN: 4812

European-Finnish (FIN) AF: 0.363 AC: 3825 AN: 10548

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28709 AN: 67964

Other (OTH) AF: 0.523 AC: 1103 AN: 2110

Alfa AF: 0.446 Hom.: 33209

Bravo AF: 0.496

Asia WGS AF: 0.588 AC: 2047 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.015
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3112625; hg19: chr16-52625552;