rs1002486

Variant names:

• chr3-34581429-A-C
• rs1002486
• ENST00000659779.1:n.379-86708A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-34581429-A-C
• chr3-34581429-A-G
• chr3-34581429-A-T

Variant summary

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

The ENST00000659779.1(LINC01811):​n.379-86708A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,586 control chromosomes in the GnomAD database, including 5,127 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 0.23 (5127 hom., cov: 32)
• Consequence: LINC01811 ENST00000659779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 3 publications found

Genes affected

LINC01811 (HGNC:52615): (long intergenic non-protein coding RNA 1811)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659779.1. 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
	LINC01811	ENST00000659779.1		n.379-86708A>C		intron	N/A
	LINC01811	ENST00000669904.1		n.240-86708A>C		intron	N/A
	LINC01811	ENST00000721494.1		n.587+29859A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35291 AN: 151468 Hom.: 5120 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.233 AC: 35328 AN: 151586 Hom.: 5127 Cov.: 32 AF XY: 0.237 AC XY: 17553 AN XY: 74060

African (AFR) AF: 0.371 AC: 15348 AN: 41376

American (AMR) AF: 0.302 AC: 4581 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.0812 AC: 281 AN: 3462

East Asian (EAS) AF: 0.461 AC: 2354 AN: 5104

South Asian (SAS) AF: 0.220 AC: 1057 AN: 4814

European-Finnish (FIN) AF: 0.198 AC: 2097 AN: 10592

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9019 AN: 67752

Other (OTH) AF: 0.212 AC: 445 AN: 2102

Alfa AF: 0.160 Hom.: 3811

Bravo AF: 0.252

Asia WGS AF: 0.276 AC: 957 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.67
PhyloP100		0.58

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1002486;

hg19: chr3-34622921;

COSMIC: COSV70043780;