chr1-244013122-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440494.1. 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
	LINC02774	NR_033883.1		n.750+2202G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02774	ENST00000440494.1	TSL:1	n.750+2202G>T		intron	N/A
	LINC02774	ENST00000652928.1		n.482+2202G>T		intron	N/A
	LINC02774	ENST00000806721.1		n.322-28305G>T		intron	N/A

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

African (AFR) AF: 0.220 AC: 9100 AN: 41372

American (AMR) AF: 0.431 AC: 6585 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1738 AN: 3462

East Asian (EAS) AF: 0.228 AC: 1176 AN: 5156

South Asian (SAS) AF: 0.495 AC: 2384 AN: 4818

European-Finnish (FIN) AF: 0.507 AC: 5315 AN: 10490

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34050 AN: 67932

Other (OTH) AF: 0.402 AC: 848 AN: 2110

Alfa AF: 0.461 Hom.: 46796

Bravo AF: 0.390

Asia WGS AF: 0.342 AC: 1190 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.48
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs476141; hg19: chr1-244176424;