rs2390582

Variant names:

• chr1-90478350-A-G
• rs2390582
• ENST00000779570.1:n.194+418T>C

Variant summary

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

The ENST00000779570.1(LINC02787):​n.194+418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,036 control chromosomes in the GnomAD database, including 2,217 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 0.15 (2217 hom., cov: 32)
• Consequence: LINC02787 ENST00000779570.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 12 publications found

Genes affected

LINC02787 (HGNC:54308): (long intergenic non-protein coding RNA 2787)

LOC105378851 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779570.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02787	ENST00000779570.1		n.194+418T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23407 AN: 151918 Hom.: 2206 Cov.: 32

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.154 AC: 23429 AN: 152036 Hom.: 2217 Cov.: 32 AF XY: 0.160 AC XY: 11868 AN XY: 74320

African (AFR) AF: 0.0833 AC: 3461 AN: 41524

American (AMR) AF: 0.281 AC: 4292 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3464

East Asian (EAS) AF: 0.334 AC: 1722 AN: 5162

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4820

European-Finnish (FIN) AF: 0.158 AC: 1665 AN: 10532

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10143 AN: 67958

Other (OTH) AF: 0.175 AC: 369 AN: 2110

Alfa AF: 0.160 Hom.: 4012

Bravo AF: 0.161

Asia WGS AF: 0.310 AC: 1075 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.87
PhyloP100		1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2390582;

hg19: chr1-90943907;

COSMIC: COSV59971789;