chr16-52623613-T-C

Variant names:

• chr16-52623613-T-C
• rs3104807
• ENST00000563844.1:n.312+7337A>G

Variant summary

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

The ENST00000563844.1(CASC16):​n.312+7337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,702 control chromosomes in the GnomAD database, including 9,919 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 0.34 (9919 hom., cov: 31)
• Consequence: CASC16 ENST00000563844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 2 publications found

Genes affected

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

ENSG00000261261 (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 (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563844.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000563844.1	TSL:3	n.312+7337A>G		intron	N/A
	ENSG00000261261	ENST00000564331.1	TSL:3	n.53+719T>C		intron	N/A
	ENSG00000261261	ENST00000565229.2	TSL:3	n.780+719T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50948 AN: 151582 Hom.: 9921 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.336 AC: 50950 AN: 151702 Hom.: 9919 Cov.: 31 AF XY: 0.339 AC XY: 25123 AN XY: 74100

African (AFR) AF: 0.131 AC: 5418 AN: 41468

American (AMR) AF: 0.349 AC: 5328 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1628 AN: 3460

East Asian (EAS) AF: 0.447 AC: 2297 AN: 5134

South Asian (SAS) AF: 0.314 AC: 1508 AN: 4800

European-Finnish (FIN) AF: 0.455 AC: 4756 AN: 10462

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28765 AN: 67806

Other (OTH) AF: 0.348 AC: 735 AN: 2114

Alfa AF: 0.388 Hom.: 30258

Bravo AF: 0.321

Asia WGS AF: 0.365 AC: 1271 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	6.6
DANN	Benign	0.79
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs3104807; hg19: chr16-52657525;