2-181287104-C-G

Position:

• chr2-181287104-C-G

Variant summary

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

The ENST00000424655.1(LINC01934):​n.105-53942C>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 ENST00000424655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

Genes affected

LINC01934 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.358+24127C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000424170.5	n.412-871C>G		intron_variant		4
LINC01934	ENST00000424655.1	n.105-53942C>G		intron_variant		3
LINC01934	ENST00000428474.5	n.150+60569C>G		intron_variant		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

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.391

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720453; hg19: chr2-182151831;