rs16906415

Variant names:

• chr8-136837768-A-G
• rs16906415
• ENST00000521034.1:n.98+40398A>G

Variant summary

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

The ENST00000521034.1(LINC02055):​n.98+40398A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 151,932 control chromosomes in the GnomAD database, including 1,078 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 0.093 (1078 hom., cov: 32)
• Consequence: LINC02055 ENST00000521034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02055	NR_147196.1	n.443+40398A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000521034.1	n.98+40398A>G		intron_variant	Intron 1 of 3	5
LINC02055	ENST00000521097.5	n.153+40398A>G		intron_variant	Intron 2 of 4	5
LINC02055	ENST00000524346.6	n.470+40398A>G		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14129 AN: 151814 Hom.: 1081 Cov.: 32

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0930 AC: 14134 AN: 151932 Hom.: 1078 Cov.: 32 AF XY: 0.0949 AC XY: 7042 AN XY: 74238

African (AFR) AF: 0.0270 AC: 1120 AN: 41540

American (AMR) AF: 0.121 AC: 1844 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1317 AN: 5170

South Asian (SAS) AF: 0.179 AC: 852 AN: 4764

European-Finnish (FIN) AF: 0.0984 AC: 1042 AN: 10588

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7094 AN: 67846

Other (OTH) AF: 0.111 AC: 233 AN: 2102

Alfa AF: 0.103 Hom.: 590

Bravo AF: 0.0923

Asia WGS AF: 0.188 AC: 652 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.85
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs16906415; hg19: chr8-137850011;