rs3104798

Variant names:

• chr16-52610983-C-G
• rs3104798
• ENST00000564361.2:n.845C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

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_184331.1		n.852C>G		non_coding_transcript_exon	Exon 3 of 3
	LINC03064	NR_184332.1		n.805C>G		non_coding_transcript_exon	Exon 2 of 2
	LINC03064	NR_184333.1		n.931C>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03064	ENST00000564361.2	TSL:3	n.845C>G		non_coding_transcript_exon	Exon 3 of 3
	LINC03064	ENST00000655643.1		n.781C>G		non_coding_transcript_exon	Exon 2 of 2
	LINC03064	ENST00000659772.1		n.750C>G		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.585 AC: 24246 AN: 41466

American (AMR) AF: 0.558 AC: 8525 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4096 AN: 5184

South Asian (SAS) AF: 0.462 AC: 2230 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3369 AN: 10540

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28747 AN: 67968

Other (OTH) AF: 0.536 AC: 1132 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs3104798; hg19: chr16-52644895;