2-181287104-C-G

Variant names:

• chr2-181287104-C-G
• rs720453
• ENST00000424170.5:n.412-871C>G

Variant summary

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

The ENST00000424170.5(LINC01934):​n.412-871C>G 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 151,290 control chromosomes in the GnomAD database, including 11,853 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 (11853 hom., cov: 32)
• Consequence: LINC01934 ENST00000424170.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• 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=-0.97).
• 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+24127C>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000424170.5	n.412-871C>G		intron_variant	Intron 3 of 5	4
LINC01934	ENST00000424655.1	n.105-53942C>G		intron_variant	Intron 2 of 3	3
LINC01934	ENST00000428474.5	n.150+60569C>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59232 AN: 151174 Hom.: 11848 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.392 AC: 59258 AN: 151290 Hom.: 11853 Cov.: 32 AF XY: 0.386 AC XY: 28566 AN XY: 73962

African (AFR) AF: 0.361 AC: 14776 AN: 40902

American (AMR) AF: 0.349 AC: 5320 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1485 AN: 3464

East Asian (EAS) AF: 0.388 AC: 2005 AN: 5174

South Asian (SAS) AF: 0.328 AC: 1579 AN: 4820

European-Finnish (FIN) AF: 0.364 AC: 3834 AN: 10534

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.426 AC: 28917 AN: 67868

Other (OTH) AF: 0.391 AC: 823 AN: 2106

Alfa AF: 0.244 Hom.: 574

Bravo AF: 0.391

Asia WGS AF: 0.302 AC: 1050 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.41
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs720453; hg19: chr2-182151831;