1-218459583-T-G

Position:

• chr1-218459583-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663551.1(LINC02869):​n.87+232T>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02869	ENST00000663551.1	n.87+232T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.231

Alfa AF: 0.213 Hom.: 7223

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11118109; hg19: chr1-218632925;