2-107281738-C-G

Variant summary

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

The NR_183814.1(LINC01789):n.95-15030G>C 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 0.809 in 152,166 control chromosomes in the GnomAD database, including 50,429 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 0.81 (50429 hom., cov: 33)
• Consequence: LINC01789 NR_183814.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

LINC01789 (HGNC:52578): (long intergenic non-protein coding RNA 1789)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01789	NR_183814.1	n.95-15030G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01789	ENST00000443123.1	n.395-15030G>C		intron_variant, non_coding_transcript_variant		5
LINC01789	ENST00000455614.1	n.235+301G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123091 AN: 152050 Hom.: 50410 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.809 AC: 123146 AN: 152166 Hom.: 50429 Cov.: 33 AF XY: 0.814 AC XY: 60536 AN XY: 74398

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.835

Alfa AF: 0.824 Hom.: 6451

Bravo AF: 0.802

Asia WGS AF: 0.885 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.9
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7578096; hg19: chr2-107898194;