rs3012465

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-133029797-A-G
• chr6-133029797-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC00326	ENST00000659399.1	n.211-32369A>G		intron_variant	Intron 2 of 2
LINC00326	ENST00000668229.1	n.72-57983A>G		intron_variant	Intron 1 of 2
LINC00326	ENST00000669115.2	n.205+75197A>G		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.715

Alfa AF: 0.676 Hom.: 16937

Bravo AF: 0.741

Asia WGS AF: 0.828 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3012465; hg19: chr6-133350936;