8-136928848-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000521034.1	n.192+31770A>G		intron_variant	Intron 2 of 3	5
LINC02055	ENST00000649576.1	n.564+31770A>G		intron_variant	Intron 5 of 8
LINC02055	ENST00000663759.1	n.537+31770A>G		intron_variant	Intron 5 of 5
LINC02055	ENST00000669387.1	n.507+31770A>G		intron_variant	Intron 5 of 6

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

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.950

Alfa AF: 0.967 Hom.: 30855

Bravo AF: 0.933

Asia WGS AF: 0.953 AC: 3314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs981457; hg19: chr8-137941091;