rs17356983

Variant names:

• chr13-21340975-A-G
• rs17356983
• ENST00000411525.1:n.388+3691T>C

Variant summary

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

The ENST00000411525.1(LINC00539):​n.388+3691T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,004 control chromosomes in the GnomAD database, including 4,986 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 0.25 (4986 hom., cov: 32)
• Consequence: LINC00539 ENST00000411525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 5 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIPEPP3	NR_046461.1	n.439-10173A>G		intron_variant	Intron 2 of 4
LINC00539	NR_103840.1	n.121+3691T>C		intron_variant	Intron 1 of 5
LINC00539	NR_103841.1	n.194+3691T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00539	ENST00000411525.1	n.388+3691T>C		intron_variant	Intron 3 of 4	3
LINC00539	ENST00000423575.6	n.389+3691T>C		intron_variant	Intron 1 of 2	3
LINC00539	ENST00000434601.7	n.388+3691T>C		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37476 AN: 151886 Hom.: 4973 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.247 AC: 37512 AN: 152004 Hom.: 4986 Cov.: 32 AF XY: 0.239 AC XY: 17753 AN XY: 74320

African (AFR) AF: 0.288 AC: 11940 AN: 41452

American (AMR) AF: 0.184 AC: 2811 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3466

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5180

South Asian (SAS) AF: 0.183 AC: 880 AN: 4814

European-Finnish (FIN) AF: 0.196 AC: 2068 AN: 10560

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 17987 AN: 67932

Other (OTH) AF: 0.246 AC: 519 AN: 2108

Alfa AF: 0.257 Hom.: 11030

Bravo AF: 0.247

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.31
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs17356983; hg19: chr13-21915114;