rs2454222

Variant names:

• chr1-244029798-G-A
• rs2454222
• ENST00000440494.1:n.1053+2364G>A

Variant summary

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

The ENST00000440494.1(LINC02774):​n.1053+2364G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,758 control chromosomes in the GnomAD database, including 29,042 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 0.60 (29042 hom., cov: 30)
• Consequence: LINC02774 ENST00000440494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 2 publications found

Genes affected

LINC02774 (HGNC:27923): (long intergenic non-protein coding RNA 2774)

ENSG00000289055 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02774	NR_033883.1	n.1053+2364G>A		intron_variant	Intron 8 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02774	ENST00000440494.1	n.1053+2364G>A		intron_variant	Intron 8 of 11	1
LINC02774	ENST00000806721.1	n.322-11629G>A		intron_variant	Intron 2 of 3
LINC02774	ENST00000806722.1	n.859+2364G>A		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90819 AN: 151638 Hom.: 28995 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.599 AC: 90928 AN: 151758 Hom.: 29042 Cov.: 30 AF XY: 0.600 AC XY: 44454 AN XY: 74128

African (AFR) AF: 0.830 AC: 34387 AN: 41426

American (AMR) AF: 0.575 AC: 8777 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3468

East Asian (EAS) AF: 0.750 AC: 3864 AN: 5154

South Asian (SAS) AF: 0.502 AC: 2411 AN: 4802

European-Finnish (FIN) AF: 0.483 AC: 5035 AN: 10422

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32871 AN: 67918

Other (OTH) AF: 0.620 AC: 1306 AN: 2108

Alfa AF: 0.541 Hom.: 37915

Bravo AF: 0.618

Asia WGS AF: 0.634 AC: 2199 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.28
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs2454222; hg19: chr1-244193100;