1-90848953-T-C

Variant summary

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

The NR_135038.1(LINC02609):n.156+2530A>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 0.537 in 151,940 control chromosomes in the GnomAD database, including 22,132 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 0.54 (22132 hom., cov: 32)
• Consequence: LINC02609 NR_135038.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

LINC02788 (HGNC:54309): (long intergenic non-protein coding RNA 2788)

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02609	NR_135038.1	n.156+2530A>G		intron_variant, non_coding_transcript_variant
LINC02609	NR_147930.1	n.168+2530A>G		intron_variant, non_coding_transcript_variant
LINC02609	NR_147931.1	n.168+2530A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02788	ENST00000662449.1	n.473-36T>C		intron_variant, non_coding_transcript_variant
LINC02609	ENST00000671059.1	n.46+2530A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81565 AN: 151822 Hom.: 22126 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.537 AC: 81623 AN: 151940 Hom.: 22132 Cov.: 32 AF XY: 0.538 AC XY: 39926 AN XY: 74276

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.547

Alfa AF: 0.538 Hom.: 10804

Bravo AF: 0.539

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1766163; hg19: chr1-91314510;