ENST00000667534.1:n.212-8928A>G

Variant names:

• chr13-105787017-A-G
• rs7327673
• ENST00000667534.1:n.212-8928A>G

Variant summary

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

The ENST00000667534.1(LINC00343):​n.212-8928A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,090 control chromosomes in the GnomAD database, including 41,873 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 0.74 (41873 hom., cov: 32)
• Consequence: LINC00343 ENST00000667534.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 2 publications found

Genes affected

LINC00343 (HGNC:42500): (long intergenic non-protein coding RNA 343)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667534.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00343	ENST00000667534.1		n.212-8928A>G		intron	N/A
	LINC00343	ENST00000669840.1		n.224-8379A>G		intron	N/A
	LINC00343	ENST00000831894.1		n.211-8928A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112407 AN: 151972 Hom.: 41844 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.740 AC: 112484 AN: 152090 Hom.: 41873 Cov.: 32 AF XY: 0.733 AC XY: 54495 AN XY: 74336

African (AFR) AF: 0.700 AC: 29040 AN: 41490

American (AMR) AF: 0.691 AC: 10550 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2559 AN: 3472

East Asian (EAS) AF: 0.530 AC: 2739 AN: 5164

South Asian (SAS) AF: 0.659 AC: 3178 AN: 4826

European-Finnish (FIN) AF: 0.771 AC: 8165 AN: 10588

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53771 AN: 67974

Other (OTH) AF: 0.739 AC: 1562 AN: 2114

Alfa AF: 0.772 Hom.: 176747

Bravo AF: 0.731

Asia WGS AF: 0.642 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.30
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs7327673; hg19: chr13-106439366;