ENST00000659399.1:n.211-32369A>G

Variant names:

• chr6-133029797-A-G
• rs3012465
• ENST00000659399.1:n.211-32369A>G

Variant summary

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

The ENST00000659399.1(LINC00326):​n.211-32369A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,184 control chromosomes in the GnomAD database, including 41,300 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 0.73 (41300 hom., cov: 33)
• Consequence: LINC00326 ENST00000659399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 16 publications found

Genes affected

LINC00326 (HGNC:41926): (long intergenic non-protein coding RNA 326)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659399.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00326	ENST00000659399.1		n.211-32369A>G		intron	N/A
	LINC00326	ENST00000668229.2		n.72-57983A>G		intron	N/A
	LINC00326	ENST00000669115.3		n.284+75197A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110741 AN: 152066 Hom.: 41246 Cov.: 33

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.728 AC: 110855 AN: 152184 Hom.: 41300 Cov.: 33 AF XY: 0.731 AC XY: 54415 AN XY: 74402

African (AFR) AF: 0.869 AC: 36102 AN: 41528

American (AMR) AF: 0.754 AC: 11533 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1984 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4538 AN: 5174

South Asian (SAS) AF: 0.795 AC: 3838 AN: 4828

European-Finnish (FIN) AF: 0.648 AC: 6852 AN: 10574

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.644 AC: 43814 AN: 67998

Other (OTH) AF: 0.715 AC: 1512 AN: 2114

Alfa AF: 0.673 Hom.: 61396

Bravo AF: 0.741

Asia WGS AF: 0.828 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.22
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3012465; hg19: chr6-133350936;