rs10490266

Positions:

• chr2-40752860-C-G
• chr2-40752860-C-T

Variant summary

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

The NR_183396.1(LINC01794):​n.633-1706C>G 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 0.47 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 NR_183396.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

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

LOC105374497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01794	NR_183396.1	n.633-1706C>G		intron_variant, non_coding_transcript_variant
LOC105374497	XR_001739421.3	n.217-55933G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01794	ENST00000420187.1	n.167-1706C>G		intron_variant, non_coding_transcript_variant		4
LINC01794	ENST00000655021.1	n.173-1706C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.486

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490266; hg19: chr2-40980000;