chr1-244024298-A-G

Variant names:

• chr1-244024298-A-G
• rs1000543
• ENST00000440494.1:n.751-668A>G

Variant summary

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

The ENST00000440494.1(LINC02774):​n.751-668A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,014 control chromosomes in the GnomAD database, including 30,957 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 0.62 (30957 hom., cov: 32)
• Consequence: LINC02774 ENST00000440494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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.751-668A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02774	ENST00000440494.1	TSL:1	n.751-668A>G		intron	N/A
	LINC02774	ENST00000652928.1		n.483-635A>G		intron	N/A
	LINC02774	ENST00000806721.1		n.322-17129A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93484 AN: 151896 Hom.: 30904 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.616 AC: 93599 AN: 152014 Hom.: 30957 Cov.: 32 AF XY: 0.618 AC XY: 45900 AN XY: 74290

African (AFR) AF: 0.857 AC: 35584 AN: 41500

American (AMR) AF: 0.594 AC: 9075 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3468

East Asian (EAS) AF: 0.820 AC: 4240 AN: 5170

South Asian (SAS) AF: 0.505 AC: 2428 AN: 4810

European-Finnish (FIN) AF: 0.524 AC: 5523 AN: 10538

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

European-Non Finnish (NFE) AF: 0.488 AC: 33123 AN: 67930

Other (OTH) AF: 0.632 AC: 1333 AN: 2110

Alfa AF: 0.524 Hom.: 35266

Bravo AF: 0.635

Asia WGS AF: 0.663 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.7
DANN	Benign	0.66
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs1000543; hg19: chr1-244187600;