ENST00000420187.2:n.172-1706C>G

Variant names:

• chr2-40752860-C-G
• rs10490266
• ENST00000420187.2:n.172-1706C>G

Variant summary

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

The ENST00000420187.2(LINC01794):​n.172-1706C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,998 control chromosomes in the GnomAD database, including 19,089 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 0.47 (19089 hom., cov: 32)
• Consequence: LINC01794 ENST00000420187.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 3 publications found

Genes affected

LINC01794 (HGNC:52584): (long intergenic non-protein coding RNA 1794)

ENSG00000298207 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420187.2. 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
	LINC01794	NR_183395.1		n.173-1706C>G		intron	N/A
	LINC01794	NR_183396.1		n.633-1706C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01794	ENST00000420187.2	TSL:4	n.172-1706C>G		intron	N/A
	LINC01794	ENST00000655021.2		n.174-1706C>G		intron	N/A
	ENSG00000298207	ENST00000753888.1		n.307-55933G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71438 AN: 151880 Hom.: 19099 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.470 AC: 71435 AN: 151998 Hom.: 19089 Cov.: 32 AF XY: 0.474 AC XY: 35219 AN XY: 74282

African (AFR) AF: 0.209 AC: 8660 AN: 41410

American (AMR) AF: 0.494 AC: 7544 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1857 AN: 5168

South Asian (SAS) AF: 0.689 AC: 3327 AN: 4826

European-Finnish (FIN) AF: 0.614 AC: 6490 AN: 10564

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39758 AN: 67970

Other (OTH) AF: 0.486 AC: 1028 AN: 2114

Alfa AF: 0.394 Hom.: 1238

Bravo AF: 0.446

Asia WGS AF: 0.472 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10490266; hg19: chr2-40980000;