2-107281738-C-G

Variant names:

• chr2-107281738-C-G
• rs7578096
• ENST00000443123.1:n.395-15030G>C

Variant summary

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

The ENST00000455614.1(LINC01789):​n.235+301G>C variant causes a intron 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 ENST00000455614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455614.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01789	NR_183814.1		n.95-15030G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01789	ENST00000443123.1	TSL:5	n.395-15030G>C		intron	N/A
	LINC01789	ENST00000455614.1	TSL:3	n.235+301G>C		intron	N/A

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

African (AFR) AF: 0.684 AC: 28362 AN: 41478

American (AMR) AF: 0.845 AC: 12918 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3034 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4980 AN: 5164

South Asian (SAS) AF: 0.870 AC: 4200 AN: 4830

European-Finnish (FIN) AF: 0.889 AC: 9431 AN: 10610

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57583 AN: 68010

Other (OTH) AF: 0.835 AC: 1760 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7578096; hg19: chr2-107898194;