rs1766167

chr1-90836250-A-G

Variant summary

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

The NR_135038.1(LINC02609):n.156+15233T>C 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 0.281 in 152,138 control chromosomes in the GnomAD database, including 6,205 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 0.28 (6202 hom., cov: 33)
  • Exomes 𝑓: 0.42 (3 hom.)
• Consequence: LINC02609 NR_135038.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02609	NR_135038.1	n.156+15233T>C		intron_variant, non_coding_transcript_variant
LINC02609	NR_147930.1	n.169-4054T>C		intron_variant, non_coding_transcript_variant
LINC02609	NR_147931.1	n.384+1300T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02788	ENST00000662449.1	n.260+331A>G		intron_variant, non_coding_transcript_variant
LINC02609	ENST00000671059.1	n.46+15233T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42690 AN: 151998 Hom.: 6205 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.417 AC: 10 AN: 24 Hom.: 3 AF XY: 0.450 AC XY: 9 AN XY: 20

Gnomad4 NFE exome AF: 0.455

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.281 AC: 42700 AN: 152114 Hom.: 6202 Cov.: 33 AF XY: 0.280 AC XY: 20787 AN XY: 74352

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.291

Alfa AF: 0.271 Hom.: 6222

Bravo AF: 0.288

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.1
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1766167; hg19: chr1-91301807;