1-244013122-G-T

Variant names:

• chr1-244013122-G-T
• rs476141
• ENST00000440494.1:n.750+2202G>T

Variant summary

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

The ENST00000440494.1(LINC02774):​n.750+2202G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,814 control chromosomes in the GnomAD database, including 13,894 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 0.41 (13894 hom., cov: 31)
• Consequence: LINC02774 ENST00000440494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02774	NR_033883.1	n.750+2202G>T		intron_variant	Intron 6 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02774	ENST00000440494.1	n.750+2202G>T		intron_variant	Intron 6 of 11	1
LINC02774	ENST00000652928.1	n.482+2202G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61687 AN: 151696 Hom.: 13894 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.406 AC: 61699 AN: 151814 Hom.: 13894 Cov.: 31 AF XY: 0.409 AC XY: 30328 AN XY: 74194

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.402

Alfa AF: 0.472 Hom.: 34818

Bravo AF: 0.390

Asia WGS AF: 0.342 AC: 1190 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs476141; hg19: chr1-244176424;