rs7015122

Variant names:

• chr8-136130669-A-G
• rs7015122
• ENST00000502901.6:n.186-31806A>G

Variant summary

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

The ENST00000502901.6(LINC02055):​n.186-31806A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,138 control chromosomes in the GnomAD database, including 4,085 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 0.21 (4085 hom., cov: 33)
• Consequence: LINC02055 ENST00000502901.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 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.186-31806A>G		intron_variant	Intron 1 of 3	4
LINC02055	ENST00000523150.1	n.331-31806A>G		intron_variant	Intron 2 of 4	5
LINC02055	ENST00000648077.2	n.283+41463A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32467 AN: 152020 Hom.: 4085 Cov.: 33

Gnomad AFR AF: 0.0986

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.213 AC: 32476 AN: 152138 Hom.: 4085 Cov.: 33 AF XY: 0.221 AC XY: 16462 AN XY: 74342

Gnomad4 AFR AF: 0.0986

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.181

Alfa AF: 0.234 Hom.: 760

Bravo AF: 0.190

Asia WGS AF: 0.275 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7015122; hg19: chr8-137142912;