2-107261224-C-G

Position:

• chr2-107261224-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.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

Genes affected

LINC01789 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01789	NR_183814.1	n.369+3504G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01789	ENST00000443123.1	n.669+3504G>C		intron_variant		5

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

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.849

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9308906; hg19: chr2-107877680;