ENST00000652561.2:n.299+15661T>A

Variant names:

• chr2-67374839-A-T
• rs6739392
• ENST00000652561.2:n.299+15661T>A

Variant summary

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

The ENST00000652561.2(LINC01829):​n.299+15661T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,144 control chromosomes in the GnomAD database, including 33,631 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 0.66 (33631 hom., cov: 33)
• Consequence: LINC01829 ENST00000652561.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815
• Publications: 12 publications found

Genes affected

LINC01829 (HGNC:52635): (long intergenic non-protein coding RNA 1829)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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
LINC01829	ENST00000652561.2	n.299+15661T>A		intron_variant	Intron 3 of 9
LINC01829	ENST00000821349.1	n.232+23081T>A		intron_variant	Intron 1 of 7
LINC01829	ENST00000821350.1	n.217+23081T>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100183 AN: 152026 Hom.: 33593 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.659 AC: 100281 AN: 152144 Hom.: 33631 Cov.: 33 AF XY: 0.656 AC XY: 48772 AN XY: 74360

African (AFR) AF: 0.777 AC: 32263 AN: 41524

American (AMR) AF: 0.654 AC: 9993 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2369 AN: 3472

East Asian (EAS) AF: 0.577 AC: 2984 AN: 5176

South Asian (SAS) AF: 0.655 AC: 3162 AN: 4824

European-Finnish (FIN) AF: 0.542 AC: 5726 AN: 10574

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41547 AN: 67980

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.629 Hom.: 3795

Bravo AF: 0.672

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.9
DANN	Benign	0.79
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs6739392; hg19: chr2-67601971;