ENST00000841191.1:n.463A>G

Variant names:

• chr6-2651753-A-G
• rs9328112
• ENST00000841191.1:n.463A>G

Variant summary

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

The ENST00000841191.1(LINC02521):​n.463A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,068 control chromosomes in the GnomAD database, including 22,354 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 0.53 (22354 hom., cov: 32)
• Consequence: LINC02521 ENST00000841191.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• Publications: 2 publications found

Genes affected

LINC02521 (HGNC:53560): (long intergenic non-protein coding RNA 2521)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841191.1. 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
	LINC02521	ENST00000841191.1		n.463A>G		non_coding_transcript_exon	Exon 2 of 2
	LINC02521	ENST00000841192.1		n.379A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80819 AN: 151948 Hom.: 22334 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.532 AC: 80878 AN: 152068 Hom.: 22354 Cov.: 32 AF XY: 0.538 AC XY: 40034 AN XY: 74344

African (AFR) AF: 0.366 AC: 15194 AN: 41472

American (AMR) AF: 0.568 AC: 8686 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2976 AN: 5166

South Asian (SAS) AF: 0.654 AC: 3152 AN: 4820

European-Finnish (FIN) AF: 0.596 AC: 6301 AN: 10566

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40793 AN: 67974

Other (OTH) AF: 0.554 AC: 1168 AN: 2110

Alfa AF: 0.565 Hom.: 14760

Bravo AF: 0.518

Asia WGS AF: 0.590 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.53
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs9328112; hg19: chr6-2651987;