chr8-137087023-C-T

Variant names:

• chr8-137087023-C-T
• rs7007075
• ENST00000649576.1:n.795-3387C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649576.1(LINC02055):​n.795-3387C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.764
• Publications: 1 publications found

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000649576.1	n.795-3387C>T		intron_variant	Intron 7 of 8
LINC02055	ENST00000837562.1	n.482-3387C>T		intron_variant	Intron 5 of 6

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

African (AFR) AF: 0.792 AC: 32838 AN: 41476

American (AMR) AF: 0.402 AC: 6124 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3466

East Asian (EAS) AF: 0.626 AC: 3214 AN: 5136

South Asian (SAS) AF: 0.439 AC: 2118 AN: 4820

European-Finnish (FIN) AF: 0.326 AC: 3431 AN: 10520

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26469 AN: 67898

Other (OTH) AF: 0.457 AC: 963 AN: 2106

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
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs7007075; hg19: chr8-138099266;