chr13-21344705-G-A

Position:

• chr13-21344705-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00539 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00539	NR_103840.1	n.82C>T		non_coding_transcript_exon_variant	1/6
LINC00539	NR_103841.1	n.155C>T		non_coding_transcript_exon_variant	1/3
MIPEPP3	NR_046461.1	n.439-6443G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00539	ENST00000411525.1	n.349C>T		non_coding_transcript_exon_variant	3/5	3
LINC00539	ENST00000423575.5	n.141C>T		non_coding_transcript_exon_variant	1/3	3
LINC00539	ENST00000434601.7	n.349C>T		non_coding_transcript_exon_variant	3/7	5

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

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.751

Gnomad4 NFE exome AF: 0.694

Gnomad4 OTH exome AF: 0.660

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

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.628

Alfa AF: 0.667 Hom.: 15261

Bravo AF: 0.616

Asia WGS AF: 0.679 AC: 2361 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	2.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7336525; hg19: chr13-21918844;