chr8-136025273-A-G

Variant names:

• chr8-136025273-A-G
• rs2317355
• ENST00000650054.1:n.250+13086A>G

Variant summary

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

The ENST00000650054.1(LINC02055):​n.250+13086A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,644 control chromosomes in the GnomAD database, including 28,043 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 0.60 (28043 hom., cov: 33)
• Consequence: LINC02055 ENST00000650054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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	ENST00000650054.1	n.250+13086A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91592 AN: 151522 Hom.: 28024 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.724

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.604 AC: 91658 AN: 151644 Hom.: 28043 Cov.: 33 AF XY: 0.602 AC XY: 44556 AN XY: 74070

African (AFR) AF: 0.512 AC: 21208 AN: 41384

American (AMR) AF: 0.584 AC: 8908 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2526 AN: 3466

East Asian (EAS) AF: 0.486 AC: 2496 AN: 5134

South Asian (SAS) AF: 0.588 AC: 2830 AN: 4816

European-Finnish (FIN) AF: 0.611 AC: 6393 AN: 10466

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.666 AC: 45181 AN: 67828

Other (OTH) AF: 0.628 AC: 1320 AN: 2102

Alfa AF: 0.617 Hom.: 5046

Bravo AF: 0.599

Asia WGS AF: 0.556 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.50
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2317355; hg19: chr8-137037516;