chr2-181143073-T-C

Variant names:

• chr2-181143073-T-C
• rs1018326
• ENST00000414750.1:n.259+19093T>C

Variant summary

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

The ENST00000414750.1(LINC01934):​n.259+19093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,942 control chromosomes in the GnomAD database, including 17,684 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 0.48 (17684 hom., cov: 32)
• Consequence: LINC01934 ENST00000414750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570
• Publications: 39 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.144+19093T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000414750.1	n.259+19093T>C		intron_variant	Intron 4 of 4	3
LINC01934	ENST00000424170.5	n.146+19093T>C		intron_variant	Intron 1 of 5	4
LINC01934	ENST00000424655.1	n.39+19093T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72175 AN: 151828 Hom.: 17658 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.475 AC: 72242 AN: 151942 Hom.: 17684 Cov.: 32 AF XY: 0.484 AC XY: 35971 AN XY: 74262

African (AFR) AF: 0.470 AC: 19491 AN: 41440

American (AMR) AF: 0.549 AC: 8385 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3468

East Asian (EAS) AF: 0.733 AC: 3798 AN: 5184

South Asian (SAS) AF: 0.623 AC: 3002 AN: 4822

European-Finnish (FIN) AF: 0.501 AC: 5272 AN: 10530

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.437 AC: 29662 AN: 67912

Other (OTH) AF: 0.463 AC: 978 AN: 2112

Alfa AF: 0.449 Hom.: 25199

Bravo AF: 0.477

Asia WGS AF: 0.696 AC: 2407 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.78
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1018326; hg19: chr2-182007800;