rs2660664

Variant names:

• chr8-136514080-G-A
• rs2660664
• ENST00000523232.3:n.179-1886G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-136514080-G-A
• chr8-136514080-G-C

Variant summary

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

The ENST00000523232.3(LINC02055):​n.179-1886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,614 control chromosomes in the GnomAD database, including 37,297 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 0.69 (37297 hom., cov: 29)
• Consequence: LINC02055 ENST00000523232.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 1 publications found

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

LOC124900255 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523232.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02055	ENST00000523232.3	TSL:4	n.179-1886G>A		intron	N/A
	LINC02055	ENST00000650445.3		n.239-1345G>A		intron	N/A
	LINC02055	ENST00000650470.1		n.405-1886G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105024 AN: 151492 Hom.: 37250 Cov.: 29

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.693 AC: 105127 AN: 151614 Hom.: 37297 Cov.: 29 AF XY: 0.695 AC XY: 51451 AN XY: 74054

African (AFR) AF: 0.850 AC: 35153 AN: 41356

American (AMR) AF: 0.671 AC: 10195 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2122 AN: 3466

East Asian (EAS) AF: 0.779 AC: 3974 AN: 5100

South Asian (SAS) AF: 0.749 AC: 3597 AN: 4804

European-Finnish (FIN) AF: 0.644 AC: 6753 AN: 10482

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41244 AN: 67888

Other (OTH) AF: 0.687 AC: 1450 AN: 2112

Alfa AF: 0.635 Hom.: 15931

Bravo AF: 0.700

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.67
PhyloP100		-0.88

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: rs2660664;

hg19: chr8-137526323;