chr8-136928848-A-G

Variant names:

• chr8-136928848-A-G
• rs981457
• ENST00000521034.1:n.192+31770A>G

Variant summary

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

The ENST00000521034.1(LINC02055):​n.192+31770A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,140 control chromosomes in the GnomAD database, including 67,622 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 0.94 (67622 hom., cov: 31)
• Consequence: LINC02055 ENST00000521034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521034.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02055	ENST00000521034.1	TSL:5	n.192+31770A>G		intron	N/A
	LINC02055	ENST00000649576.1		n.564+31770A>G		intron	N/A
	LINC02055	ENST00000663759.1		n.537+31770A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143144 AN: 152022 Hom.: 67559 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.942 AC: 143264 AN: 152140 Hom.: 67622 Cov.: 31 AF XY: 0.943 AC XY: 70168 AN XY: 74372

African (AFR) AF: 0.873 AC: 36223 AN: 41476

American (AMR) AF: 0.952 AC: 14533 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3309 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4686 AN: 5150

South Asian (SAS) AF: 0.989 AC: 4773 AN: 4828

European-Finnish (FIN) AF: 0.987 AC: 10483 AN: 10620

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66110 AN: 68010

Other (OTH) AF: 0.950 AC: 2003 AN: 2108

Alfa AF: 0.967 Hom.: 34487

Bravo AF: 0.933

Asia WGS AF: 0.953 AC: 3314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.31
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs981457; hg19: chr8-137941091;