rs6577710

Variant names:

• chr8-136128990-G-A
• rs6577710
• ENST00000502901.6:n.186-33485G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-136128990-G-A
• chr8-136128990-G-C
• chr8-136128990-G-T

Variant summary

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

The ENST00000502901.6(LINC02055):​n.186-33485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,074 control chromosomes in the GnomAD database, including 36,534 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 0.68 (36534 hom., cov: 32)
• Consequence: LINC02055 ENST00000502901.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502901.6. 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	ENST00000502901.6	TSL:4	n.186-33485G>A		intron	N/A
	LINC02055	ENST00000523150.1	TSL:5	n.331-33485G>A		intron	N/A
	LINC02055	ENST00000648077.2		n.283+39784G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103216 AN: 151954 Hom.: 36527 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.708

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.679 AC: 103265 AN: 152074 Hom.: 36534 Cov.: 32 AF XY: 0.677 AC XY: 50334 AN XY: 74344

African (AFR) AF: 0.547 AC: 22680 AN: 41442

American (AMR) AF: 0.569 AC: 8702 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2363 AN: 3472

East Asian (EAS) AF: 0.291 AC: 1502 AN: 5154

South Asian (SAS) AF: 0.677 AC: 3264 AN: 4818

European-Finnish (FIN) AF: 0.826 AC: 8757 AN: 10596

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.788 AC: 53558 AN: 67992

Other (OTH) AF: 0.651 AC: 1375 AN: 2112

Alfa AF: 0.744 Hom.: 166863

Bravo AF: 0.649

Asia WGS AF: 0.505 AC: 1757 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	1.9
DANN	Benign	0.32
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6577710; hg19: chr8-137141233;