chr16-52607274-T-A

Variant names:

• chr16-52607274-T-A
• rs3104793
• ENST00000564361.2:n.208T>A

Variant summary

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

The ENST00000564361.2(LINC03064):​n.208T>A variant causes a non coding transcript exon 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: 33)
• Consequence: LINC03064 ENST00000564361.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 17 publications found

Genes affected

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

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

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=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564361.2. 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
	LINC03064	NR_184325.1		n.215T>A		non_coding_transcript_exon	Exon 1 of 3
	LINC03064	NR_184326.1		n.215T>A		non_coding_transcript_exon	Exon 1 of 3
	LINC03064	NR_184331.1		n.215T>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03064	ENST00000564361.2	TSL:3	n.208T>A		non_coding_transcript_exon	Exon 1 of 3
	LINC03064	ENST00000565153.2	TSL:2	n.253T>A		non_coding_transcript_exon	Exon 1 of 3
	LINC03064	ENST00000655643.1		n.223T>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3104793; hg19: chr16-52641186;