rs12036718

chr1-48083641-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635446.1(LINC02794):n.541-306G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02794	XR_007066068.1	n.1429-306G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02794	ENST00000635446.1	n.541-306G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.117

Alfa AF: 0.151 Hom.: 1871

Bravo AF: 0.119

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.0
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12036718; hg19: chr1-48549313;