rs7835148

Variant names:

• chr8-135889742-G-A
• rs7835148
• ENST00000648045.1:n.227+5963G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-135889742-G-A
• chr8-135889742-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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000648045.1	n.227+5963G>A		intron_variant	Intron 2 of 2
LINC02055	ENST00000650217.1	n.227+5963G>A		intron_variant	Intron 2 of 3

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;