rs12563333

Variant names:

• chr1-220484892-C-T
• rs12563333
• NR_185879.1:n.1026G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_185879.1(LINC02779):​n.1026G>A 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 0.0377 in 152,270 control chromosomes in the GnomAD database, including 142 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 0.038 (142 hom., cov: 32)
• Consequence: LINC02779 NR_185879.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 8 publications found

Genes affected

LINC02779 (HGNC:54299): (long intergenic non-protein coding RNA 2779)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.083 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02779	NR_185879.1	n.1026G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02779	ENST00000785452.1	n.559+2099G>A		intron_variant	Intron 1 of 1
LINC02779	ENST00000785453.1	n.255+2383G>A		intron_variant	Intron 1 of 1
LINC02779	ENST00000785456.1	n.537+2099G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0377 AC: 5729 AN: 152152 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0198

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0377 AC: 5738 AN: 152270 Hom.: 142 Cov.: 32 AF XY: 0.0377 AC XY: 2807 AN XY: 74442

African (AFR) AF: 0.0482 AC: 2003 AN: 41550

American (AMR) AF: 0.0198 AC: 303 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3470

East Asian (EAS) AF: 0.0897 AC: 464 AN: 5170

South Asian (SAS) AF: 0.0596 AC: 287 AN: 4818

European-Finnish (FIN) AF: 0.0314 AC: 333 AN: 10610

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0301 AC: 2050 AN: 68024

Other (OTH) AF: 0.0378 AC: 80 AN: 2116

Alfa AF: 0.0327 Hom.: 282

Bravo AF: 0.0371

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.51
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs12563333; hg19: chr1-220658234;