ENST00000650054.1:n.58+7538C>T

Variant names:

• chr8-135976961-C-T
• rs16905439
• ENST00000650054.1:n.58+7538C>T

Variant summary

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

The ENST00000650054.1(LINC02055):​n.58+7538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 152,130 control chromosomes in the GnomAD database, including 1,195 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 0.081 (1195 hom., cov: 33)
• Consequence: LINC02055 ENST00000650054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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.58+7538C>T		intron_variant	Intron 1 of 5
LINC02055	ENST00000650217.1	n.555-35035C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0806 AC: 12251 AN: 152012 Hom.: 1188 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0807 AC: 12276 AN: 152130 Hom.: 1195 Cov.: 33 AF XY: 0.0796 AC XY: 5922 AN XY: 74382

African (AFR) AF: 0.226 AC: 9357 AN: 41474

American (AMR) AF: 0.0463 AC: 707 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.123 AC: 638 AN: 5168

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4826

European-Finnish (FIN) AF: 0.00188 AC: 20 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1114 AN: 67996

Other (OTH) AF: 0.0699 AC: 148 AN: 2116

Alfa AF: 0.0378 Hom.: 1021

Bravo AF: 0.0910

Asia WGS AF: 0.0970 AC: 335 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.46
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs16905439; hg19: chr8-136989204;