2-181131318-A-G

Variant summary

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

The NR_130784.1(LINC01934):n.144+7338A>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 0.476 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 NR_130784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01934	NR_130784.1	n.144+7338A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01934	ENST00000435411.6	n.144+7338A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.461

Alfa AF: 0.450 Hom.: 23958

Bravo AF: 0.476

Asia WGS AF: 0.706 AC: 2451 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.0
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13010713; hg19: chr2-181996045;