rs2639277

Variant names:

• chr3-81043537-A-G
• rs2639277
• ENST00000482617.4:n.198+16576A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NR_132411.1(LINC02027):​n.60+49610A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_132411.1. 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
	LINC02027	NR_132411.1		n.60+49610A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02027	ENST00000482617.4	TSL:5	n.198+16576A>G		intron	N/A
	LINC02027	ENST00000653347.3		n.102+49610A>G		intron	N/A
	LINC02027	ENST00000662919.2		n.118-1827A>G		intron	N/A

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

African (AFR) AF: 0.594 AC: 24601 AN: 41424

American (AMR) AF: 0.706 AC: 10785 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2834 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3160 AN: 5128

South Asian (SAS) AF: 0.764 AC: 3671 AN: 4804

European-Finnish (FIN) AF: 0.783 AC: 8278 AN: 10578

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52965 AN: 67978

Other (OTH) AF: 0.729 AC: 1540 AN: 2112

Alfa AF: 0.739 Hom.: 7086

Bravo AF: 0.700

Asia WGS AF: 0.702 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.59
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2639277; hg19: chr3-81092688;