rs11679180

Variant names:

• chr2-228777706-G-A
• rs11679180
• ENST00000665053.1:n.76-33014C>T

Variant summary

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

The ENST00000665053.1(LINC01807):​n.76-33014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,536 control chromosomes in the GnomAD database, including 2,922 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 0.19 (2922 hom., cov: 32)
• Consequence: LINC01807 ENST00000665053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 4 publications found

Genes affected

LINC01807 (HGNC:52610): (long intergenic non-protein coding RNA 1807)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665053.1. 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
	LINC01807	ENST00000665053.1		n.76-33014C>T		intron	N/A
	LINC01807	ENST00000667233.2		n.321-33014C>T		intron	N/A
	LINC01807	ENST00000787811.1		n.302-33018C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28414 AN: 151416 Hom.: 2920 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.188 AC: 28427 AN: 151536 Hom.: 2922 Cov.: 32 AF XY: 0.182 AC XY: 13500 AN XY: 74038

African (AFR) AF: 0.107 AC: 4413 AN: 41138

American (AMR) AF: 0.161 AC: 2459 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1085 AN: 5114

South Asian (SAS) AF: 0.171 AC: 820 AN: 4792

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10560

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16712 AN: 67906

Other (OTH) AF: 0.203 AC: 426 AN: 2102

Alfa AF: 0.225 Hom.: 6858

Bravo AF: 0.183

Asia WGS AF: 0.171 AC: 595 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.22
DANN	Benign	0.36
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs11679180; hg19: chr2-229642422;