ENST00000455680.5:n.2941A>G

Variant names:

• chr1-90829592-T-C
• rs941031
• ENST00000455680.5:n.2941A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455680.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02609	NR_147930.1		n.2773A>G		non_coding_transcript_exon	Exon 2 of 2
	LINC02609	NR_147931.1		n.2989A>G		non_coding_transcript_exon	Exon 3 of 3
	LINC02609	NR_147932.1		n.2941A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02609	ENST00000455680.5	TSL:1	n.2941A>G		non_coding_transcript_exon	Exon 2 of 2
	LINC02609	ENST00000606660.1	TSL:2	n.2741A>G		non_coding_transcript_exon	Exon 2 of 2
	LINC02609	ENST00000658618.4		n.2824A>G		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.229 AC: 9491 AN: 41514

American (AMR) AF: 0.501 AC: 7638 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2025 AN: 3464

East Asian (EAS) AF: 0.335 AC: 1733 AN: 5180

South Asian (SAS) AF: 0.497 AC: 2400 AN: 4826

European-Finnish (FIN) AF: 0.592 AC: 6246 AN: 10556

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39641 AN: 67910

Other (OTH) AF: 0.485 AC: 1023 AN: 2110

Alfa AF: 0.557 Hom.: 15628

Bravo AF: 0.446

Asia WGS AF: 0.392 AC: 1361 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.9
DANN	Benign	0.68
PhyloP100		0.0090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs941031;

hg19: chr1-91295149;