rs3104798

Positions:

• chr16-52610983-C-G
• chr16-52610983-C-T

Variant summary

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

The ENST00000564361.2(LINC03064):​n.845C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,052 control chromosomes in the GnomAD database, including 19,266 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 (19266 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC03064 ENST00000564361.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03064	NR_184331.1	n.852C>G		non_coding_transcript_exon_variant	3/3
LINC03064	NR_184332.1	n.805C>G		non_coding_transcript_exon_variant	2/2
LINC03064	NR_184333.1	n.931C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03064	ENST00000564361.2	n.845C>G		non_coding_transcript_exon_variant	3/3	3
LINC03064	ENST00000655643.1	n.781C>G		non_coding_transcript_exon_variant	2/2
LINC03064	ENST00000659772.1	n.750C>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74627 AN: 151934 Hom.: 19219 Cov.: 33

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.533

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.491 AC: 74729 AN: 152052 Hom.: 19266 Cov.: 33 AF XY: 0.487 AC XY: 36225 AN XY: 74326

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.536

Alfa AF: 0.452 Hom.: 1929

Bravo AF: 0.514

Asia WGS AF: 0.599 AC: 2086 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3104798; hg19: chr16-52644895;