rs11809337

Variant names:

• chr1-229122474-G-A
• rs11809337
• ENST00000662083.1:n.47-29186C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-229122474-G-A
• chr1-229122474-G-T

Variant summary

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

The ENST00000662083.1(LINC02814):​n.47-29186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,100 control chromosomes in the GnomAD database, including 3,906 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 0.17 (3906 hom., cov: 32)
• Consequence: LINC02814 ENST00000662083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 0 publications found

Genes affected

LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

LINC02815 (HGNC:54347): (long intergenic non-protein coding RNA 2815)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02815	NR_186725.1	n.157-29186C>T		intron_variant	Intron 1 of 3
LINC02815	NR_186726.1	n.157-29186C>T		intron_variant	Intron 1 of 2
LINC02815	NR_186727.1	n.544+252C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02814	ENST00000662083.1	n.47-29186C>T		intron_variant	Intron 1 of 4
LINC02814	ENST00000666388.1	n.338-29186C>T		intron_variant	Intron 2 of 2
LINC02814	ENST00000716797.1	n.184-29186C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26327 AN: 151982 Hom.: 3896 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.173 AC: 26368 AN: 152100 Hom.: 3906 Cov.: 32 AF XY: 0.168 AC XY: 12480 AN XY: 74368

African (AFR) AF: 0.403 AC: 16715 AN: 41442

American (AMR) AF: 0.133 AC: 2039 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3470

East Asian (EAS) AF: 0.0268 AC: 139 AN: 5180

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4820

European-Finnish (FIN) AF: 0.0493 AC: 523 AN: 10600

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0872 AC: 5929 AN: 67994

Other (OTH) AF: 0.154 AC: 324 AN: 2108

Alfa AF: 0.0704 Hom.: 128

Bravo AF: 0.189

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.45
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11809337; hg19: chr1-229258221;