rs1566039

Positions:

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

Variant summary

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

The NR_146281.1(LINC02236):​n.467-4842G>A 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 0.373 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 NR_146281.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02236	NR_146281.1	n.467-4842G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02236	ENST00000691419.1	n.715-4842G>A		intron_variant, non_coding_transcript_variant
LINC02236	ENST00000508881.1	n.467-4842G>A		intron_variant, non_coding_transcript_variant		4
LINC02236	ENST00000648399.1	n.498-4842G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.334

Alfa AF: 0.352 Hom.: 14627

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1566039; hg19: chr5-6821914;