rs722743

Variant names:

• chr8-136279436-A-G
• rs722743
• ENST00000648077.2:n.398-13814A>G

Variant summary

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

The ENST00000648077.2(LINC02055):​n.398-13814A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,994 control chromosomes in the GnomAD database, including 25,632 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 0.57 (25632 hom., cov: 32)
• Consequence: LINC02055 ENST00000648077.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

ENSG00000285683 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 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	ENST00000648077.2	n.398-13814A>G		intron_variant	Intron 3 of 4
LINC02055	ENST00000650445.2	n.98+81093A>G		intron_variant	Intron 1 of 7
ENSG00000285683	ENST00000660704.1	n.111+15686T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87100 AN: 151876 Hom.: 25604 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.573 AC: 87167 AN: 151994 Hom.: 25632 Cov.: 32 AF XY: 0.577 AC XY: 42831 AN XY: 74292

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.579

Alfa AF: 0.614 Hom.: 5898

Bravo AF: 0.563

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.098
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: rs722743; hg19: chr8-137291679;