rs2454222

Positions:

• chr1-244029798-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033883.1(LINC02774):​n.1053+2364G>A variant causes a intron, non coding transcript 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 NR_033883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02774	NR_033883.1	n.1053+2364G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02774	ENST00000440494.1	n.1053+2364G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.620

Alfa AF: 0.506 Hom.: 21975

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2454222; hg19: chr1-244193100;