1-90781472-T-G

Position:

• chr1-90781472-T-G

Variant summary

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

The ENST00000671059.1(LINC02609):​n.136+7926A>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 0.301 in 151,838 control chromosomes in the GnomAD database, including 8,319 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 (8319 hom., cov: 31)
• Consequence: LINC02609 ENST00000671059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680

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=-0.73).
• 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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02609	ENST00000671059.1	n.136+7926A>C		intron_variant, non_coding_transcript_variant
LINC02609	ENST00000659034.3	n.2228A>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45755 AN: 151722 Hom.: 8323 Cov.: 31

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.301 AC: 45756 AN: 151838 Hom.: 8319 Cov.: 31 AF XY: 0.305 AC XY: 22605 AN XY: 74178

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.311

Alfa AF: 0.369 Hom.: 4445

Bravo AF: 0.285

Asia WGS AF: 0.287 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3856228; hg19: chr1-91247029;