rs7007075

Positions:

• chr8-137087023-C-T

Variant summary

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

The ENST00000649576.1(LINC02055):​n.795-3387C>T 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 0.509 in 151,878 control chromosomes in the GnomAD database, including 22,227 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 0.51 (22227 hom., cov: 32)
• Consequence: LINC02055 ENST00000649576.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.764

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 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	ENST00000649576.1	n.795-3387C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77166 AN: 151760 Hom.: 22199 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.509 AC: 77240 AN: 151878 Hom.: 22227 Cov.: 32 AF XY: 0.503 AC XY: 37286 AN XY: 74196

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.457

Alfa AF: 0.454 Hom.: 2215

Bravo AF: 0.527

Asia WGS AF: 0.555 AC: 1926 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7007075; hg19: chr8-138099266;