rs6577710

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000502901.6	n.186-33485G>A		intron_variant, non_coding_transcript_variant		4
LINC02055	ENST00000523150.1	n.331-33485G>A		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000648077.2	n.283+39784G>A		intron_variant, non_coding_transcript_variant

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;