rs10505661

Variant names:

• chr8-136638959-A-C
• rs10505661
• ENST00000517345.6:n.84+101900A>C

Variant summary

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

The ENST00000517345.6(LINC02055):​n.84+101900A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 152,208 control chromosomes in the GnomAD database, including 961 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 0.075 (961 hom., cov: 33)
• Consequence: LINC02055 ENST00000517345.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 0 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02055	NR_147196.1	n.291+101900A>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000517345.6	n.84+101900A>C		intron_variant	Intron 1 of 3	3
LINC02055	ENST00000520060.3	n.345-92360A>C		intron_variant	Intron 2 of 2	4
LINC02055	ENST00000524346.6	n.318+101900A>C		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11425 AN: 152088 Hom.: 953 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.00433

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0752 AC: 11451 AN: 152208 Hom.: 961 Cov.: 33 AF XY: 0.0736 AC XY: 5474 AN XY: 74410

African (AFR) AF: 0.196 AC: 8130 AN: 41498

American (AMR) AF: 0.0774 AC: 1182 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3470

East Asian (EAS) AF: 0.0740 AC: 384 AN: 5188

South Asian (SAS) AF: 0.0157 AC: 76 AN: 4828

European-Finnish (FIN) AF: 0.00433 AC: 46 AN: 10618

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1212 AN: 68012

Other (OTH) AF: 0.0819 AC: 173 AN: 2112

Alfa AF: 0.0503 Hom.: 66

Bravo AF: 0.0861

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.1
DANN	Benign	0.58
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10505661; hg19: chr8-137651202;