rs1566039

Variant names:

• chr5-6821801-G-A
• rs1566039
• ENST00000508881.1:n.467-4842G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-6821801-G-A
• chr5-6821801-G-C
• chr5-6821801-G-T

Variant summary

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

The ENST00000508881.1(LINC02236):​n.467-4842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,094 control chromosomes in the GnomAD database, including 10,989 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 0.37 (10989 hom., cov: 33)
• Consequence: LINC02236 ENST00000508881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 14 publications found

Genes affected

LINC02236 (HGNC:53107): (long intergenic non-protein coding RNA 2236)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02236	NR_146281.1	n.467-4842G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02236	ENST00000508881.1	n.467-4842G>A		intron_variant	Intron 1 of 1	4
LINC02236	ENST00000648399.1	n.498-4842G>A		intron_variant	Intron 3 of 6
LINC02236	ENST00000691419.2	n.715-4842G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56677 AN: 151976 Hom.: 10980 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.373 AC: 56718 AN: 152094 Hom.: 10989 Cov.: 33 AF XY: 0.380 AC XY: 28224 AN XY: 74350

African (AFR) AF: 0.351 AC: 14572 AN: 41490

American (AMR) AF: 0.402 AC: 6147 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3705 AN: 5178

South Asian (SAS) AF: 0.397 AC: 1912 AN: 4822

European-Finnish (FIN) AF: 0.415 AC: 4382 AN: 10564

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23889 AN: 67974

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.360 Hom.: 36024

Bravo AF: 0.374

Asia WGS AF: 0.531 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.55
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1566039; hg19: chr5-6821914;