16-52590826-G-T

Variant names:

• chr16-52590826-G-T
• rs3104767
• ENST00000510238.9:n.621+110C>A

Variant summary

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

The ENST00000510238.9(CASC16):​n.621+110C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,026 control chromosomes in the GnomAD database, including 19,321 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 0.49 (19321 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 38 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=-0.96).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	NR_033920.1		n.604+110C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.621+110C>A		intron	N/A
	CASC16	ENST00000563844.1	TSL:3	n.444+110C>A		intron	N/A
	CASC16	ENST00000565755.2	TSL:3	n.342+110C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74905 AN: 151908 Hom.: 19278 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.493 AC: 75005 AN: 152026 Hom.: 19321 Cov.: 32 AF XY: 0.491 AC XY: 36464 AN XY: 74304

African (AFR) AF: 0.583 AC: 24167 AN: 41448

American (AMR) AF: 0.556 AC: 8506 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1837 AN: 3468

East Asian (EAS) AF: 0.784 AC: 4054 AN: 5172

South Asian (SAS) AF: 0.459 AC: 2206 AN: 4806

European-Finnish (FIN) AF: 0.358 AC: 3788 AN: 10568

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28705 AN: 67960

Other (OTH) AF: 0.536 AC: 1134 AN: 2114

Alfa AF: 0.449 Hom.: 33409

Bravo AF: 0.513

Asia WGS AF: 0.592 AC: 2061 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3104767;

hg19: chr16-52624738;