rs2639277

Positions:

• chr3-81043537-A-G
• chr3-81043537-A-T

Variant summary

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

The NR_132411.1(LINC02027):​n.60+49610A>G 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 0.716 in 151,970 control chromosomes in the GnomAD database, including 39,412 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 0.72 (39412 hom., cov: 32)
• Consequence: LINC02027 NR_132411.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

LINC02027 (HGNC:52862): (long intergenic non-protein coding RNA 2027)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02027	NR_132411.1	n.60+49610A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02027	ENST00000666491.1	n.49+49610A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108748 AN: 151852 Hom.: 39406 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.716 AC: 108791 AN: 151970 Hom.: 39412 Cov.: 32 AF XY: 0.718 AC XY: 53337 AN XY: 74292

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.729

Alfa AF: 0.743 Hom.: 6945

Bravo AF: 0.700

Asia WGS AF: 0.702 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2639277; hg19: chr3-81092688;