rs10505659

Variant names:

• chr8-136449370-A-G
• rs10505659
• ENST00000650445.3:n.239-66055A>G

Variant summary

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

The ENST00000650445.3(LINC02055):​n.239-66055A>G variant causes a intron 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 ENST00000650445.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• 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=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000650445.3	n.239-66055A>G		intron_variant	Intron 2 of 7

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

African (AFR) AF: 0.287 AC: 11903 AN: 41492

American (AMR) AF: 0.213 AC: 3249 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.182 AC: 943 AN: 5174

South Asian (SAS) AF: 0.185 AC: 892 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1297 AN: 10612

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13777 AN: 67986

Other (OTH) AF: 0.227 AC: 480 AN: 2112

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10505659; hg19: chr8-137461613;