rs11683197

Variant names:

• chr2-64800490-T-C
• rs11683197
• ENST00000772000.1:n.441+13158A>G

Variant summary

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

The ENST00000772000.1(LINC01800):​n.441+13158A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,182 control chromosomes in the GnomAD database, including 4,303 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 0.22 (4303 hom., cov: 32)
• Consequence: LINC01800 ENST00000772000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 5 publications found

Genes affected

LINC01800 (HGNC:52590): (long intergenic non-protein coding RNA 1800)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772000.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01800	ENST00000772000.1		n.441+13158A>G		intron	N/A
	LINC01800	ENST00000772002.1		n.322+13158A>G		intron	N/A
	LINC01800	ENST00000772003.1		n.210+13207A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34157 AN: 152064 Hom.: 4301 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.225 AC: 34172 AN: 152182 Hom.: 4303 Cov.: 32 AF XY: 0.228 AC XY: 16949 AN XY: 74392

African (AFR) AF: 0.0990 AC: 4114 AN: 41540

American (AMR) AF: 0.238 AC: 3634 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3466

East Asian (EAS) AF: 0.184 AC: 951 AN: 5176

South Asian (SAS) AF: 0.407 AC: 1963 AN: 4822

European-Finnish (FIN) AF: 0.278 AC: 2945 AN: 10582

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18621 AN: 67982

Other (OTH) AF: 0.240 AC: 506 AN: 2110

Alfa AF: 0.260 Hom.: 22851

Bravo AF: 0.215

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.40
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11683197; hg19: chr2-65027624;