ENST00000435649.3:n.272+9357A>T

Variant names:

• chr1-90822573-T-A
• rs3843306
• ENST00000435649.3:n.272+9357A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435649.3(LINC02609):​n.272+9357A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,094 control chromosomes in the GnomAD database, including 10,167 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 0.33 (10167 hom., cov: 32)
• Consequence: LINC02609 ENST00000435649.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 9 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=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02609	NR_135038.1	n.156+28910A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02609	ENST00000435649.3	n.272+9357A>T		intron_variant	Intron 1 of 2	5
LINC02609	ENST00000634619.2	n.648+9357A>T		intron_variant	Intron 3 of 4	5
LINC02609	ENST00000635581.4	n.453+9357A>T		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50053 AN: 151974 Hom.: 10171 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.329 AC: 50048 AN: 152094 Hom.: 10167 Cov.: 32 AF XY: 0.331 AC XY: 24586 AN XY: 74364

African (AFR) AF: 0.0866 AC: 3595 AN: 41506

American (AMR) AF: 0.398 AC: 6072 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5168

South Asian (SAS) AF: 0.352 AC: 1698 AN: 4828

European-Finnish (FIN) AF: 0.489 AC: 5172 AN: 10578

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30080 AN: 67954

Other (OTH) AF: 0.354 AC: 747 AN: 2110

Alfa AF: 0.411 Hom.: 7413

Bravo AF: 0.310

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.8
DANN	Benign	0.87
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs3843306; hg19: chr1-91288130;