rs1868092

Variant names:

• chr2-46387063-G-A
• rs1868092
• ENST00000843948.1:n.103-39004C>T

Variant summary

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

The ENST00000843948.1(LINC01820):​n.103-39004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,126 control chromosomes in the GnomAD database, including 10,233 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 0.34 (10233 hom., cov: 33)
• Consequence: LINC01820 ENST00000843948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 20 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01820	ENST00000843948.1	n.103-39004C>T		intron_variant	Intron 1 of 1
LINC01820	ENST00000843949.1	n.126-11571C>T		intron_variant	Intron 1 of 2
LINC01820	ENST00000843950.1	n.273-11571C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52069 AN: 152008 Hom.: 10237 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.342 AC: 52065 AN: 152126 Hom.: 10233 Cov.: 33 AF XY: 0.338 AC XY: 25127 AN XY: 74362

African (AFR) AF: 0.174 AC: 7224 AN: 41510

American (AMR) AF: 0.272 AC: 4161 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3470

East Asian (EAS) AF: 0.0898 AC: 466 AN: 5188

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4818

European-Finnish (FIN) AF: 0.434 AC: 4582 AN: 10558

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31312 AN: 67972

Other (OTH) AF: 0.342 AC: 722 AN: 2110

Alfa AF: 0.408 Hom.: 29220

Bravo AF: 0.322

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.83
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1868092; hg19: chr2-46614202;