16-52610012-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000565153.2(LINC03064):​n.517+2474C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.14).

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>G		intron	N/A
	LINC03064	NR_184324.1		n.458+109C>G		intron	N/A
	LINC03064	NR_184325.1		n.479+2474C>G		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 6226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.040
DANN	Benign	0.13
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs8046994; hg19: chr16-52643924;