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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000502901.6	n.186-33485G>A		intron_variant	Intron 1 of 3	4
LINC02055	ENST00000523150.1	n.331-33485G>A		intron_variant	Intron 2 of 4	5
LINC02055	ENST00000648077.2	n.283+39784G>A		intron_variant	Intron 2 of 4

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

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.651

Alfa AF: 0.754 Hom.: 66084

Bravo AF: 0.649

Asia WGS AF: 0.505 AC: 1757 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	1.9
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6577710; hg19: chr8-137141233;