1-199369020-A-C

Variant names:

• chr1-199369020-A-C
• rs599779
• ENST00000452199.1:n.310-22301A>C

Variant summary

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

The ENST00000452199.1(LINC02789):​n.310-22301A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,744 control chromosomes in the GnomAD database, including 29,891 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 (29891 hom., cov: 31)
• Consequence: LINC02789 ENST00000452199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 3 publications found

Genes affected

LINC02789 (HGNC:54310): (long intergenic non-protein coding RNA 2789)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452199.1. 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
	LINC02789	NR_147896.1		n.310-22301A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02789	ENST00000452199.1	TSL:2	n.310-22301A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94378 AN: 151626 Hom.: 29849 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.623 AC: 94477 AN: 151744 Hom.: 29891 Cov.: 31 AF XY: 0.619 AC XY: 45850 AN XY: 74120

African (AFR) AF: 0.732 AC: 30339 AN: 41420

American (AMR) AF: 0.654 AC: 9956 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2113 AN: 3464

East Asian (EAS) AF: 0.580 AC: 2969 AN: 5116

South Asian (SAS) AF: 0.512 AC: 2468 AN: 4818

European-Finnish (FIN) AF: 0.519 AC: 5480 AN: 10550

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 38995 AN: 67840

Other (OTH) AF: 0.621 AC: 1312 AN: 2114

Alfa AF: 0.562 Hom.: 11028

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-2.2

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: rs599779;

hg19: chr1-199338148;