1-60132629-G-A

Variant names:

• chr1-60132629-G-A
• rs646860
• ENST00000456878.1:n.100-15884G>A

Variant summary

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

The ENST00000456878.1(LINC02778):​n.100-15884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,850 control chromosomes in the GnomAD database, including 35,231 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 (35231 hom., cov: 31)
• Consequence: LINC02778 ENST00000456878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02778	XR_947430.2	n.149+17656G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02778	ENST00000456878.1	n.100-15884G>A		intron_variant	Intron 1 of 2	5
LINC02778	ENST00000659925.1	n.135-215G>A		intron_variant	Intron 1 of 4
ENSG00000303283	ENST00000793364.1	n.369+101C>T		intron_variant	Intron 1 of 1
LINC02778	ENST00000793418.1	n.134-215G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103127 AN: 151732 Hom.: 35204 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.680 AC: 103200 AN: 151850 Hom.: 35231 Cov.: 31 AF XY: 0.679 AC XY: 50351 AN XY: 74206

African (AFR) AF: 0.691 AC: 28609 AN: 41404

American (AMR) AF: 0.642 AC: 9808 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2733 AN: 5142

South Asian (SAS) AF: 0.779 AC: 3745 AN: 4808

European-Finnish (FIN) AF: 0.646 AC: 6801 AN: 10530

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47079 AN: 67910

Other (OTH) AF: 0.669 AC: 1414 AN: 2114

Alfa AF: 0.686 Hom.: 4433

Bravo AF: 0.672

Asia WGS AF: 0.659 AC: 2291 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.26
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs646860; hg19: chr1-60598301;