chr8-136048070-G-A

Position:

• chr8-136048070-G-A

Variant summary

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

The ENST00000502901.6(LINC02055):​n.185+865G>A 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 0.496 in 151,990 control chromosomes in the GnomAD database, including 19,175 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 0.50 (19175 hom., cov: 32)
• Consequence: LINC02055 ENST00000502901.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 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.185+865G>A		intron_variant, non_coding_transcript_variant		4
LINC02055	ENST00000523150.1	n.159+865G>A		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000648077.2	n.112+865G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75415 AN: 151870 Hom.: 19163 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.496 AC: 75455 AN: 151990 Hom.: 19175 Cov.: 32 AF XY: 0.499 AC XY: 37090 AN XY: 74290

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.499

Alfa AF: 0.519 Hom.: 3499

Bravo AF: 0.491

Asia WGS AF: 0.634 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12546080; hg19: chr8-137060313;