rs722743

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ENSG00000285683 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000650445.3	n.98+81093A>G		intron_variant	Intron 1 of 7
ENSG00000285683	ENST00000660704.2	n.181+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

African (AFR) AF: 0.440 AC: 18240 AN: 41442

American (AMR) AF: 0.582 AC: 8892 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2393 AN: 3466

East Asian (EAS) AF: 0.571 AC: 2944 AN: 5154

South Asian (SAS) AF: 0.702 AC: 3387 AN: 4826

European-Finnish (FIN) AF: 0.623 AC: 6577 AN: 10552

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42864 AN: 67972

Other (OTH) AF: 0.579 AC: 1219 AN: 2106

Alfa AF: 0.612 Hom.: 9991

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs722743; hg19: chr8-137291679;