rs7835148

chr8-135889742-G-Achr8-135889742-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648045.1(LINC02055):n.227+5963G>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 0.778 in 152,016 control chromosomes in the GnomAD database, including 46,817 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 0.78 (46817 hom., cov: 31)
• Consequence: LINC02055 ENST00000648045.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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	ENST00000648045.1	n.227+5963G>A		intron_variant, non_coding_transcript_variant
LINC02055	ENST00000650217.1	n.227+5963G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118201 AN: 151898 Hom.: 46760 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.778 AC: 118316 AN: 152016 Hom.: 46817 Cov.: 31 AF XY: 0.782 AC XY: 58074 AN XY: 74288

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.754

Alfa AF: 0.740 Hom.: 7130

Bravo AF: 0.785

Asia WGS AF: 0.793 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.90
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7835148; hg19: chr8-136901985;