1-90829592-T-C

Position:

• chr1-90829592-T-C

Variant summary

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

The ENST00000455680.5(LINC02609):​n.2941A>G 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 0.466 in 152,020 control chromosomes in the GnomAD database, including 18,372 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 0.47 (18372 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC02609 ENST00000455680.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

LINC02609 (HGNC:27140): (long intergenic non-protein coding RNA 2609)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02609	NR_135038.1	n.156+21891A>G		intron_variant, non_coding_transcript_variant
LINC02609	NR_147930.1	n.2773A>G		non_coding_transcript_exon_variant	2/2
LINC02609	NR_147931.1	n.2989A>G		non_coding_transcript_exon_variant	3/3
LINC02609	NR_147932.1	n.2941A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02609	ENST00000671059.1	n.46+21891A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70761 AN: 151900 Hom.: 18380 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.489

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.466 AC: 70770 AN: 152020 Hom.: 18372 Cov.: 33 AF XY: 0.466 AC XY: 34606 AN XY: 74298

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.485

Alfa AF: 0.560 Hom.: 13192

Bravo AF: 0.446

Asia WGS AF: 0.392 AC: 1361 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941031; hg19: chr1-91295149;