rs17356983

Positions:

• chr13-21340975-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00539 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MIPEPP3	NR_046461.1	n.439-10173A>G		intron_variant
LINC00539	NR_103840.1	n.121+3691T>C		intron_variant
LINC00539	NR_103841.1	n.194+3691T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00539	ENST00000411525.1	n.388+3691T>C		intron_variant		3
LINC00539	ENST00000423575.5	n.180+3691T>C		intron_variant		3
LINC00539	ENST00000434601.7	n.388+3691T>C		intron_variant		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

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.246

Alfa AF: 0.258 Hom.: 7010

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17356983; hg19: chr13-21915114;