rs12036718

Variant names:

• chr1-48083641-G-A
• rs12036718
• ENST00000635446.1:n.541-306G>A

Variant summary

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

The ENST00000635446.1(LINC02794):​n.541-306G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,142 control chromosomes in the GnomAD database, including 1,540 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 0.13 (1540 hom., cov: 32)
• Consequence: LINC02794 ENST00000635446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 3 publications found

Genes affected

LINC02794 (HGNC:54318): (long intergenic non-protein coding RNA 2794)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635446.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02794	ENST00000635446.1	TSL:3	n.541-306G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19179 AN: 152024 Hom.: 1538 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.126 AC: 19185 AN: 152142 Hom.: 1540 Cov.: 32 AF XY: 0.128 AC XY: 9502 AN XY: 74362

African (AFR) AF: 0.0315 AC: 1309 AN: 41534

American (AMR) AF: 0.127 AC: 1948 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3468

East Asian (EAS) AF: 0.151 AC: 779 AN: 5158

South Asian (SAS) AF: 0.175 AC: 841 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1965 AN: 10570

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11316 AN: 67994

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.138 Hom.: 2620

Bravo AF: 0.119

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.43
PhyloP100		0.49

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: rs12036718;

hg19: chr1-48549313;