rs3012465

Positions:

• 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 ENST00000670892.1(LINC00326):​n.327-57983A>G variant causes a intron, non coding transcript 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 ENST00000670892.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00326	ENST00000670892.1	n.327-57983A>G		intron_variant, non_coding_transcript_variant

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;