rs7336525

Variant names:

• chr13-21344705-G-A
• rs7336525
• ENST00000411525.1:n.349C>T

Variant summary

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

The ENST00000411525.1(LINC00539):​n.349C>T 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 0.641 in 166,768 control chromosomes in the GnomAD database, including 35,023 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 0.63 (30901 hom., cov: 33)
  • Exomes 𝑓: 0.75 (4122 hom.)
• Consequence: LINC00539 ENST00000411525.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 7 publications found

Genes affected

LINC00539 (HGNC:43672): (long intergenic non-protein coding RNA 539)

ENSG00000291046 (HGNC:):

MIPEPP3 (HGNC:39458): (mitochondrial intermediate peptidase pseudogene 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411525.1. 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
	LINC00539	NR_103840.1		n.82C>T		non_coding_transcript_exon	Exon 1 of 6
	LINC00539	NR_103841.1		n.155C>T		non_coding_transcript_exon	Exon 1 of 3
	MIPEPP3	NR_046461.1		n.439-6443G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00539	ENST00000411525.1	TSL:3	n.349C>T		non_coding_transcript_exon	Exon 3 of 5
	LINC00539	ENST00000423575.6	TSL:3	n.350C>T		non_coding_transcript_exon	Exon 1 of 3
	LINC00539	ENST00000434601.7	TSL:5	n.349C>T		non_coding_transcript_exon	Exon 3 of 7

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95860 AN: 151976 Hom.: 30885 Cov.: 33

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.623

GnomAD4 exome AF: 0.749 AC: 10995 AN: 14674 Hom.: 4122 Cov.: 0 AF XY: 0.751 AC XY: 5229 AN XY: 6966

African (AFR) AF: 0.333 AC: 2 AN: 6

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.751 AC: 10823 AN: 14418

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.694 AC: 93 AN: 134

Other (OTH) AF: 0.660 AC: 70 AN: 106

GnomAD4 genome AF: 0.631 AC: 95917 AN: 152094 Hom.: 30901 Cov.: 33 AF XY: 0.635 AC XY: 47225 AN XY: 74344

African (AFR) AF: 0.488 AC: 20241 AN: 41466

American (AMR) AF: 0.686 AC: 10489 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3470

East Asian (EAS) AF: 0.663 AC: 3424 AN: 5162

South Asian (SAS) AF: 0.716 AC: 3451 AN: 4818

European-Finnish (FIN) AF: 0.751 AC: 7950 AN: 10584

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46166 AN: 67974

Other (OTH) AF: 0.628 AC: 1328 AN: 2114

Alfa AF: 0.663 Hom.: 22500

Bravo AF: 0.616

Asia WGS AF: 0.679 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7336525;

hg19: chr13-21918844;