rs16906415

Positions:

• chr8-136837768-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147196.1(LINC02055):​n.443+40398A>G variant causes a intron, non coding transcript 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 NR_147196.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02055	NR_147196.1	n.443+40398A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000521034.1	n.98+40398A>G		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000521097.5	n.153+40398A>G		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000524346.6	n.470+40398A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0270

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0967 Hom.: 298

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16906415; hg19: chr8-137850011;