rs2020362

Variant names:

• chr19-30850360-A-G
• rs2020362
• ENST00000716200.1:n.216-56054A>G

Variant summary

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

The ENST00000716200.1(LINC01834):​n.216-56054A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,200 control chromosomes in the GnomAD database, including 3,794 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 0.21 (3794 hom., cov: 32)
• Consequence: LINC01834 ENST00000716200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

Genes affected

LINC01834 (HGNC:52648): (long intergenic non-protein coding RNA 1834)

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 (NFE) allele frequency at 95% confidence interval = 0.276 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
LINC01834	ENST00000716200.1	n.216-56054A>G		intron_variant	Intron 1 of 2
LINC01834	ENST00000716201.1	n.165-21687A>G		intron_variant	Intron 1 of 3
LINC01834	ENST00000824349.1	n.131-21687A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31828 AN: 152082 Hom.: 3792 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.0784

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.209 AC: 31843 AN: 152200 Hom.: 3794 Cov.: 32 AF XY: 0.201 AC XY: 14923 AN XY: 74420

African (AFR) AF: 0.153 AC: 6363 AN: 41528

American (AMR) AF: 0.151 AC: 2312 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3466

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5182

South Asian (SAS) AF: 0.0785 AC: 378 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2134 AN: 10596

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18961 AN: 67994

Other (OTH) AF: 0.190 AC: 403 AN: 2116

Alfa AF: 0.255 Hom.: 632

Bravo AF: 0.203

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.43
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2020362; hg19: chr19-31341267;