1-218459583-T-G

Variant names:

• chr1-218459583-T-G
• rs11118109
• ENST00000663551.1:n.87+232T>G

Variant summary

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

The ENST00000663551.1(LINC02869):​n.87+232T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,112 control chromosomes in the GnomAD database, including 4,435 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 (4435 hom., cov: 32)
• Consequence: LINC02869 ENST00000663551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 7 publications found

Genes affected

LINC02869 (HGNC:32045): (long intergenic non-protein coding RNA 2869)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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
LINC02869	ENST00000663551.1	n.87+232T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35162 AN: 151994 Hom.: 4431 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.231 AC: 35182 AN: 152112 Hom.: 4435 Cov.: 32 AF XY: 0.229 AC XY: 17049 AN XY: 74336

African (AFR) AF: 0.309 AC: 12815 AN: 41478

American (AMR) AF: 0.180 AC: 2759 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3470

East Asian (EAS) AF: 0.0388 AC: 200 AN: 5160

South Asian (SAS) AF: 0.222 AC: 1067 AN: 4816

European-Finnish (FIN) AF: 0.210 AC: 2219 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14704 AN: 67994

Other (OTH) AF: 0.231 AC: 488 AN: 2114

Alfa AF: 0.219 Hom.: 12407

Bravo AF: 0.232

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.58
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs11118109; hg19: chr1-218632925;