rs2077783

Variant names:

• chr2-181287050-T-A
• rs2077783
• ENST00000424170.5:n.412-925T>A

Variant summary

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

The ENST00000424170.5(LINC01934):​n.412-925T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,862 control chromosomes in the GnomAD database, including 11,849 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 0.39 (11849 hom., cov: 31)
• Consequence: LINC01934 ENST00000424170.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 4 publications found

Genes affected

LINC01934 (HGNC:52757): (long intergenic non-protein coding RNA 1934)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.358+24073T>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000424170.5	n.412-925T>A		intron_variant	Intron 3 of 5	4
LINC01934	ENST00000424655.1	n.105-53996T>A		intron_variant	Intron 2 of 3	3
LINC01934	ENST00000428474.5	n.150+60515T>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59479 AN: 151746 Hom.: 11844 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.392 AC: 59505 AN: 151862 Hom.: 11849 Cov.: 31 AF XY: 0.386 AC XY: 28685 AN XY: 74238

African (AFR) AF: 0.363 AC: 15026 AN: 41394

American (AMR) AF: 0.350 AC: 5342 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3470

East Asian (EAS) AF: 0.387 AC: 2001 AN: 5174

South Asian (SAS) AF: 0.328 AC: 1580 AN: 4820

European-Finnish (FIN) AF: 0.363 AC: 3828 AN: 10548

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28896 AN: 67870

Other (OTH) AF: 0.391 AC: 827 AN: 2114

Alfa AF: 0.399 Hom.: 1559

Bravo AF: 0.391

Asia WGS AF: 0.303 AC: 1051 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.33
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs2077783; hg19: chr2-182151777;