2-181287050-T-A

Position:

• chr2-181287050-T-A

Variant summary

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

The NR_130784.1(LINC01934):​n.358+24073T>A 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 0.392 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 NR_130784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

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=-0.96).
• 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/exons	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.358+24073T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000435411.6	n.358+24073T>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.391

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077783; hg19: chr2-182151777;