rs299384

Variant names:

• chr5-17368063-G-A
• rs299384
• ENST00000653016.1:n.810C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-17368063-G-A
• chr5-17368063-G-C
• chr5-17368063-G-T

Variant summary

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

The ENST00000653016.1(ENSG00000249199):​n.810C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,064 control chromosomes in the GnomAD database, including 1,058 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 0.11 (1058 hom., cov: 31)
• Consequence: ENSG00000249199 ENST00000653016.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 publications found

Genes affected

ENSG00000249199 (HGNC:):

LINC02111 (HGNC:52966): (long intergenic non-protein coding RNA 2111)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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
ENSG00000249199	ENST00000653016.1	n.810C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000249199	ENST00000717183.1	n.999C>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000249199	ENST00000790821.1	n.1711C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17434 AN: 151944 Hom.: 1058 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.115 AC: 17448 AN: 152064 Hom.: 1058 Cov.: 31 AF XY: 0.115 AC XY: 8548 AN XY: 74320

African (AFR) AF: 0.140 AC: 5816 AN: 41478

American (AMR) AF: 0.0737 AC: 1126 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0923 AC: 320 AN: 3468

East Asian (EAS) AF: 0.137 AC: 704 AN: 5148

South Asian (SAS) AF: 0.0927 AC: 447 AN: 4820

European-Finnish (FIN) AF: 0.121 AC: 1281 AN: 10574

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7414 AN: 67972

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.107 Hom.: 1713

Bravo AF: 0.112

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs299384; hg19: chr5-17368172;