rs10922924

Positions:

• chr1-90787306-G-A

Variant summary

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

The NR_135038.1(LINC02609):​n.246+2092C>T 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 0.299 in 151,932 control chromosomes in the GnomAD database, including 8,235 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 0.30 (8235 hom., cov: 32)
• Consequence: LINC02609 NR_135038.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02609	NR_135038.1	n.246+2092C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02609	ENST00000671059.1	n.136+2092C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45361 AN: 151812 Hom.: 8238 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.299 AC: 45368 AN: 151932 Hom.: 8235 Cov.: 32 AF XY: 0.302 AC XY: 22394 AN XY: 74238

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.307

Alfa AF: 0.374 Hom.: 22819

Bravo AF: 0.281

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
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: rs10922924; hg19: chr1-91252863;