rs10495147

Variant names:

• chr1-220484221-A-G
• rs10495147
• NR_185879.1:n.1697T>C

Variant summary

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

The NR_185879.1(LINC02779):​n.1697T>C 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 0.687 in 152,150 control chromosomes in the GnomAD database, including 37,373 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 0.69 (37373 hom., cov: 32)
• Consequence: LINC02779 NR_185879.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02779	NR_185879.1	n.1697T>C		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+2770T>C		intron_variant	Intron 1 of 1
LINC02779	ENST00000785453.1	n.255+3054T>C		intron_variant	Intron 1 of 1
LINC02779	ENST00000785456.1	n.537+2770T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104490 AN: 152032 Hom.: 37374 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.687 AC: 104520 AN: 152150 Hom.: 37373 Cov.: 32 AF XY: 0.689 AC XY: 51240 AN XY: 74382

African (AFR) AF: 0.493 AC: 20465 AN: 41482

American (AMR) AF: 0.705 AC: 10775 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2513 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2728 AN: 5164

South Asian (SAS) AF: 0.729 AC: 3512 AN: 4818

European-Finnish (FIN) AF: 0.827 AC: 8763 AN: 10600

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53290 AN: 68010

Other (OTH) AF: 0.706 AC: 1492 AN: 2112

Alfa AF: 0.720 Hom.: 5023

Bravo AF: 0.664

Asia WGS AF: 0.617 AC: 2145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10495147; hg19: chr1-220657563; COSMIC: COSV71682241;