ENST00000796364.1:n.896G>A

Variant names:

• chr1-79404756-G-A
• rs10493626
• ENST00000796364.1:n.896G>A

Variant summary

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

The ENST00000796364.1(LINC02792):​n.896G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 152,148 control chromosomes in the GnomAD database, including 510 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 0.061 (510 hom., cov: 32)
• Consequence: LINC02792 ENST00000796364.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 1 publications found

Genes affected

LINC02792 (HGNC:54316): (long intergenic non-protein coding RNA 2792)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02792	ENST00000796364.1	n.896G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02792	ENST00000796356.1	n.*201G>A		downstream_gene_variant
LINC02792	ENST00000796365.1	n.*204G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9309 AN: 152030 Hom.: 507 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0613 AC: 9332 AN: 152148 Hom.: 510 Cov.: 32 AF XY: 0.0587 AC XY: 4369 AN XY: 74388

African (AFR) AF: 0.139 AC: 5763 AN: 41490

American (AMR) AF: 0.0383 AC: 584 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0127 AC: 61 AN: 4818

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10608

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0341 AC: 2320 AN: 68002

Other (OTH) AF: 0.0588 AC: 124 AN: 2108

Alfa AF: 0.0506 Hom.: 34

Bravo AF: 0.0642

Asia WGS AF: 0.0150 AC: 53 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	8.7
DANN	Benign	0.58
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10493626; hg19: chr1-79870441;