1-244033108-C-T

Variant names:

• chr1-244033108-C-T
• rs2047137
• ENST00000440494.1:n.1053+5674C>T

Variant summary

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

The ENST00000440494.1(LINC02774):​n.1053+5674C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,064 control chromosomes in the GnomAD database, including 10,712 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 0.36 (10712 hom., cov: 32)
• Consequence: LINC02774 ENST00000440494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 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.1053+5674C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02774	ENST00000440494.1	TSL:1	n.1053+5674C>T		intron	N/A
	LINC02774	ENST00000806721.1		n.322-8319C>T		intron	N/A
	LINC02774	ENST00000806722.1		n.859+5674C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54882 AN: 151946 Hom.: 10692 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.361 AC: 54944 AN: 152064 Hom.: 10712 Cov.: 32 AF XY: 0.365 AC XY: 27116 AN XY: 74326

African (AFR) AF: 0.266 AC: 11053 AN: 41478

American (AMR) AF: 0.466 AC: 7117 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3811 AN: 5168

South Asian (SAS) AF: 0.357 AC: 1719 AN: 4816

European-Finnish (FIN) AF: 0.324 AC: 3425 AN: 10578

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25114 AN: 67954

Other (OTH) AF: 0.427 AC: 901 AN: 2112

Alfa AF: 0.339 Hom.: 4641

Bravo AF: 0.370

Asia WGS AF: 0.529 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.47
PhyloP100		0.11

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: rs2047137;

hg19: chr1-244196410;