rs10505661

chr8-136638959-A-C

Variant summary

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

The NR_147196.1(LINC02055):n.291+101900A>C 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 0.0752 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 NR_147196.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80

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=-0.8).
• 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/exons	MANE	UniProt
LINC02055	NR_147196.1	n.291+101900A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000650445.2	n.918+101900A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.0740

Gnomad4 SAS AF: 0.0157

Gnomad4 FIN AF: 0.00433

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0819

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505661; hg19: chr8-137651202;