chr1-244031540-C-T

Variant names:

• chr1-244031540-C-T
• rs2454221
• ENST00000440494.1:n.1053+4106C>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+4106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,090 control chromosomes in the GnomAD database, including 30,126 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 0.61 (30126 hom., cov: 33)
• Consequence: LINC02774 ENST00000440494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02774	NR_033883.1		n.1053+4106C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02774	ENST00000440494.1	TSL:1	n.1053+4106C>T		intron	N/A
	LINC02774	ENST00000806721.1		n.322-9887C>T		intron	N/A
	LINC02774	ENST00000806722.1		n.859+4106C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92249 AN: 151972 Hom.: 30071 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.607 AC: 92365 AN: 152090 Hom.: 30126 Cov.: 33 AF XY: 0.607 AC XY: 45124 AN XY: 74340

African (AFR) AF: 0.856 AC: 35538 AN: 41518

American (AMR) AF: 0.580 AC: 8870 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3877 AN: 5178

South Asian (SAS) AF: 0.501 AC: 2416 AN: 4826

European-Finnish (FIN) AF: 0.479 AC: 5045 AN: 10536

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33022 AN: 67956

Other (OTH) AF: 0.624 AC: 1320 AN: 2116

Alfa AF: 0.538 Hom.: 27703

Bravo AF: 0.627

Asia WGS AF: 0.636 AC: 2204 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2454221; hg19: chr1-244194842;