1-90793015-A-C

Variant names:

• chr1-90793015-A-C
• rs1725390
• ENST00000435649.3:n.273-3528T>G

Variant summary

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

The ENST00000635581.4(LINC02609):​n.454-3528T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,900 control chromosomes in the GnomAD database, including 23,087 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 0.55 (23087 hom., cov: 30)
• Consequence: LINC02609 ENST00000635581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 4 publications found

Genes affected

LINC02609 (HGNC:27140): (long intergenic non-protein coding RNA 2609)

ENSG00000287076 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635581.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02609	NR_135038.1		n.157-3528T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02609	ENST00000435649.3	TSL:5	n.273-3528T>G		intron	N/A
	LINC02609	ENST00000634619.2	TSL:5	n.649-3528T>G		intron	N/A
	LINC02609	ENST00000635581.4	TSL:2	n.454-3528T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83198 AN: 151780 Hom.: 23072 Cov.: 30

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.548 AC: 83260 AN: 151900 Hom.: 23087 Cov.: 30 AF XY: 0.546 AC XY: 40519 AN XY: 74230

African (AFR) AF: 0.517 AC: 21413 AN: 41388

American (AMR) AF: 0.517 AC: 7894 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1820 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1774 AN: 5138

South Asian (SAS) AF: 0.509 AC: 2448 AN: 4814

European-Finnish (FIN) AF: 0.598 AC: 6316 AN: 10558

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.586 AC: 39827 AN: 67948

Other (OTH) AF: 0.525 AC: 1105 AN: 2106

Alfa AF: 0.567 Hom.: 71356

Bravo AF: 0.539

Asia WGS AF: 0.437 AC: 1520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.22
PhyloP100		-0.75

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1725390;

hg19: chr1-91258572;