rs10505659

chr8-136449370-A-G

Variant summary

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

The ENST00000650445.2(LINC02055):n.239-66055A>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 0.219 in 152,160 control chromosomes in the GnomAD database, including 3,844 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 0.22 (3844 hom., cov: 32)
• Consequence: LINC02055 ENST00000650445.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000650445.2	n.239-66055A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33234 AN: 152042 Hom.: 3831 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.219 AC: 33280 AN: 152160 Hom.: 3844 Cov.: 32 AF XY: 0.214 AC XY: 15890 AN XY: 74404

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.227

Alfa AF: 0.208 Hom.: 563

Bravo AF: 0.229

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505659; hg19: chr8-137461613;