16-52610012-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184326.1(LINC03064):n.480-2463C>T variant causes a intron, non coding transcript 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 NR_184326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.76

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03064	NR_184326.1	n.480-2463C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03064	ENST00000565153.2	n.517+2474C>T		intron_variant, non_coding_transcript_variant		2
CASC16	ENST00000652959.1	n.340-18945G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.450

Alfa AF: 0.380 Hom.: 3237

Bravo AF: 0.405

Asia WGS AF: 0.403 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.095
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8046994; hg19: chr16-52643924;