chr2-181131318-A-G

Variant names:

• chr2-181131318-A-G
• rs13010713
• ENST00000414750.1:n.259+7338A>G

Variant summary

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

The ENST00000414750.1(LINC01934):​n.259+7338A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,098 control chromosomes in the GnomAD database, including 17,757 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 (17757 hom., cov: 33)
• Consequence: LINC01934 ENST00000414750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 33 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414750.1. 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
	LINC01934	NR_130784.1		n.144+7338A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01934	ENST00000414750.1	TSL:3	n.259+7338A>G		intron	N/A
	LINC01934	ENST00000424170.5	TSL:4	n.146+7338A>G		intron	N/A
	LINC01934	ENST00000424655.1	TSL:3	n.39+7338A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72361 AN: 151980 Hom.: 17726 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.476 AC: 72432 AN: 152098 Hom.: 17757 Cov.: 33 AF XY: 0.485 AC XY: 36084 AN XY: 74350

African (AFR) AF: 0.471 AC: 19558 AN: 41492

American (AMR) AF: 0.542 AC: 8281 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3828 AN: 5184

South Asian (SAS) AF: 0.641 AC: 3090 AN: 4824

European-Finnish (FIN) AF: 0.498 AC: 5254 AN: 10560

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29903 AN: 67982

Other (OTH) AF: 0.461 AC: 974 AN: 2112

Alfa AF: 0.455 Hom.: 56174

Bravo AF: 0.476

Asia WGS AF: 0.706 AC: 2451 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs13010713; hg19: chr2-181996045;