chr2-107261224-C-G

Variant names:

• chr2-107261224-C-G
• rs9308906
• ENST00000443123.1:n.669+3504G>C

Variant summary

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

The NR_183814.1(LINC01789):​n.369+3504G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,056 control chromosomes in the GnomAD database, including 52,682 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 0.83 (52682 hom., cov: 30)
• Consequence: LINC01789 NR_183814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183814.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01789	NR_183814.1		n.369+3504G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01789	ENST00000443123.1	TSL:5	n.669+3504G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126201 AN: 151938 Hom.: 52664 Cov.: 30

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.830 AC: 126261 AN: 152056 Hom.: 52682 Cov.: 30 AF XY: 0.834 AC XY: 62009 AN XY: 74334

African (AFR) AF: 0.753 AC: 31203 AN: 41458

American (AMR) AF: 0.856 AC: 13086 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4960 AN: 5140

South Asian (SAS) AF: 0.895 AC: 4308 AN: 4816

European-Finnish (FIN) AF: 0.890 AC: 9421 AN: 10590

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57563 AN: 67982

Other (OTH) AF: 0.849 AC: 1792 AN: 2110

Alfa AF: 0.811 Hom.: 2910

Bravo AF: 0.826

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.69
DANN	Benign	0.71
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs9308906; hg19: chr2-107877680;