8-136928848-A-G

Position:

• chr8-136928848-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000521034.1	n.192+31770A>G		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000649576.1	n.564+31770A>G		intron_variant, non_coding_transcript_variant
LINC02055	ENST00000663759.1	n.537+31770A>G		intron_variant, non_coding_transcript_variant
LINC02055	ENST00000669387.1	n.507+31770A>G		intron_variant, non_coding_transcript_variant

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;