chr2-46415110-G-A

Variant names:

• chr2-46415110-G-A
• rs2346177
• ENST00000843945.1:n.121+13872C>T

Variant summary

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

The ENST00000843945.1(LINC01820):​n.121+13872C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,912 control chromosomes in the GnomAD database, including 19,291 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 0.50 (19291 hom., cov: 32)
• Consequence: LINC01820 ENST00000843945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 17 publications found

Genes affected

LINC01820 (HGNC:52625): (long intergenic non-protein coding RNA 1820)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843945.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01820	ENST00000843945.1		n.121+13872C>T		intron	N/A
	LINC01820	ENST00000843946.1		n.112+13872C>T		intron	N/A
	LINC01820	ENST00000843948.1		n.102+13872C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76428 AN: 151794 Hom.: 19285 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.503 AC: 76473 AN: 151912 Hom.: 19291 Cov.: 32 AF XY: 0.504 AC XY: 37416 AN XY: 74244

African (AFR) AF: 0.489 AC: 20231 AN: 41392

American (AMR) AF: 0.535 AC: 8166 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1583 AN: 3466

East Asian (EAS) AF: 0.576 AC: 2979 AN: 5176

South Asian (SAS) AF: 0.474 AC: 2289 AN: 4828

European-Finnish (FIN) AF: 0.514 AC: 5406 AN: 10516

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34298 AN: 67952

Other (OTH) AF: 0.509 AC: 1071 AN: 2106

Alfa AF: 0.506 Hom.: 91029

Bravo AF: 0.508

Asia WGS AF: 0.516 AC: 1792 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.14
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2346177; hg19: chr2-46642249;