chr16-52604591-T-C

Variant names:

• chr16-52604591-T-C
• rs3104788
• ENST00000510238.9:n.489+1913A>G

Variant summary

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

The ENST00000510238.9(CASC16):​n.489+1913A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,012 control chromosomes in the GnomAD database, including 16,884 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 0.46 (16884 hom., cov: 32)
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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.472+1913A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.489+1913A>G		intron	N/A
	CASC16	ENST00000563844.1	TSL:3	n.313-13524A>G		intron	N/A
	CASC16	ENST00000565755.2	TSL:3	n.210+1913A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70363 AN: 151894 Hom.: 16861 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.463 AC: 70431 AN: 152012 Hom.: 16884 Cov.: 32 AF XY: 0.463 AC XY: 34369 AN XY: 74304

African (AFR) AF: 0.476 AC: 19712 AN: 41440

American (AMR) AF: 0.544 AC: 8318 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3466

East Asian (EAS) AF: 0.784 AC: 4053 AN: 5168

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4814

European-Finnish (FIN) AF: 0.363 AC: 3828 AN: 10552

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28741 AN: 67962

Other (OTH) AF: 0.517 AC: 1092 AN: 2114

Alfa AF: 0.448 Hom.: 11098

Bravo AF: 0.478

Asia WGS AF: 0.581 AC: 2022 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3104788; hg19: chr16-52638503;