1-60131118-G-C

Variant names:

• chr1-60131118-G-C
• rs629962
• ENST00000456878.1:n.99+16145G>C

Variant summary

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

The ENST00000456878.1(LINC02778):​n.99+16145G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,984 control chromosomes in the GnomAD database, including 35,237 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 0.68 (35237 hom., cov: 32)
• Consequence: LINC02778 ENST00000456878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 3 publications found

Genes affected

LINC02778 (HGNC:54298): (long intergenic non-protein coding RNA 2778)

ENSG00000303283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02778	XR_947430.2	n.149+16145G>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02778	ENST00000456878.1	n.99+16145G>C		intron_variant	Intron 1 of 2	5
LINC02778	ENST00000659925.1	n.134+987G>C		intron_variant	Intron 1 of 4
ENSG00000303283	ENST00000793364.1	n.369+1612C>G		intron_variant	Intron 1 of 1
LINC02778	ENST00000793418.1	n.133+252G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103167 AN: 151866 Hom.: 35211 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.679 AC: 103239 AN: 151984 Hom.: 35237 Cov.: 32 AF XY: 0.678 AC XY: 50381 AN XY: 74286

African (AFR) AF: 0.691 AC: 28655 AN: 41486

American (AMR) AF: 0.642 AC: 9797 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2212 AN: 3468

East Asian (EAS) AF: 0.530 AC: 2728 AN: 5150

South Asian (SAS) AF: 0.778 AC: 3749 AN: 4818

European-Finnish (FIN) AF: 0.646 AC: 6814 AN: 10556

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 47075 AN: 67942

Other (OTH) AF: 0.669 AC: 1411 AN: 2108

Alfa AF: 0.589 Hom.: 1646

Bravo AF: 0.672

Asia WGS AF: 0.659 AC: 2293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.42
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs629962; hg19: chr1-60596790;