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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900255	XR_007061190.1	n.75-1886G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000523232.3	n.179-1886G>A		intron_variant	Intron 1 of 4	4
LINC02055	ENST00000650445.3	n.239-1345G>A		intron_variant	Intron 2 of 7
LINC02055	ENST00000650470.1	n.405-1886G>A		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs2660664; hg19: chr8-137526323;