rs10505648

chr8-136144207-A-Gchr8-136144207-A-T

Variant summary

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

The ENST00000502901.6(LINC02055):n.186-18268A>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 0.425 in 151,610 control chromosomes in the GnomAD database, including 14,982 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 0.43 (14982 hom., cov: 31)
• Consequence: LINC02055 ENST00000502901.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 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	ENST00000502901.6	n.186-18268A>G		intron_variant, non_coding_transcript_variant		4
LINC02055	ENST00000523150.1	n.331-18268A>G		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000648077.2	n.284-54023A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64455 AN: 151492 Hom.: 14983 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.425 AC: 64450 AN: 151610 Hom.: 14982 Cov.: 31 AF XY: 0.422 AC XY: 31284 AN XY: 74068

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.0933

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.429

Alfa AF: 0.491 Hom.: 24555

Bravo AF: 0.403

Asia WGS AF: 0.211 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.061
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505648; hg19: chr8-137156450;