chr8-136886565-C-T

Variant names:

• chr8-136886565-C-T
• rs3907170
• ENST00000521034.1:n.99-10420C>T

Variant summary

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

The ENST00000521034.1(LINC02055):​n.99-10420C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 152,280 control chromosomes in the GnomAD database, including 70,415 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 0.96 (70415 hom., cov: 34)
• Consequence: LINC02055 ENST00000521034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02055	NR_147196.1	n.444-10420C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000521034.1	n.99-10420C>T		intron_variant	Intron 1 of 3	5
LINC02055	ENST00000521097.5	n.154-1715C>T		intron_variant	Intron 2 of 4	5
LINC02055	ENST00000524346.6	n.471-10420C>T		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146293 AN: 152162 Hom.: 70353 Cov.: 34

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.961 AC: 146413 AN: 152280 Hom.: 70415 Cov.: 34 AF XY: 0.962 AC XY: 71644 AN XY: 74464

African (AFR) AF: 0.944 AC: 39237 AN: 41576

American (AMR) AF: 0.957 AC: 14600 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3307 AN: 3470

East Asian (EAS) AF: 0.910 AC: 4715 AN: 5184

South Asian (SAS) AF: 0.989 AC: 4776 AN: 4830

European-Finnish (FIN) AF: 0.987 AC: 10490 AN: 10628

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66145 AN: 68022

Other (OTH) AF: 0.964 AC: 2037 AN: 2114

Alfa AF: 0.968 Hom.: 9217

Bravo AF: 0.956

Asia WGS AF: 0.958 AC: 3330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.2
DANN	Benign	0.59
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs3907170; hg19: chr8-137898808;