16-52610012-C-T

Variant names:

• chr16-52610012-C-T
• rs8046994
• ENST00000563844.1:n.313-18945G>A

Variant summary

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

The ENST00000565153.2(LINC03064):​n.517+2474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,660 control chromosomes in the GnomAD database, including 12,364 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 0.40 (12364 hom., cov: 31)
• Consequence: LINC03064 ENST00000565153.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.76
• Publications: 10 publications found

Genes affected

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

LINC03064 (HGNC:56372): (long intergenic non-protein coding RNA 3064)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565153.2. 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
	LINC03064	NR_184323.1		n.458+109C>T		intron	N/A
	LINC03064	NR_184324.1		n.458+109C>T		intron	N/A
	LINC03064	NR_184325.1		n.479+2474C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000563844.1	TSL:3	n.313-18945G>A		intron	N/A
	LINC03064	ENST00000564361.2	TSL:3	n.552-678C>T		intron	N/A
	LINC03064	ENST00000565153.2	TSL:2	n.517+2474C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60243 AN: 151540 Hom.: 12349 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.398 AC: 60289 AN: 151660 Hom.: 12364 Cov.: 31 AF XY: 0.394 AC XY: 29217 AN XY: 74076

African (AFR) AF: 0.331 AC: 13665 AN: 41330

American (AMR) AF: 0.497 AC: 7583 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1739 AN: 3468

East Asian (EAS) AF: 0.408 AC: 2105 AN: 5154

South Asian (SAS) AF: 0.391 AC: 1873 AN: 4796

European-Finnish (FIN) AF: 0.335 AC: 3497 AN: 10448

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28305 AN: 67908

Other (OTH) AF: 0.450 AC: 944 AN: 2100

Alfa AF: 0.394 Hom.: 6226

Bravo AF: 0.405

Asia WGS AF: 0.403 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.095
DANN	Benign	0.85
PhyloP100		-4.8

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: rs8046994;

hg19: chr16-52643924;