13-83023799-A-T

Position:

• chr13-83023799-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663739.1(ENSG00000286385):​n.298+39415T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 410,860 control chromosomes in the GnomAD database, including 56,105 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 0.54 (22862 hom., cov: 31)
  • Exomes 𝑓: 0.50 (33243 hom.)
• Consequence: ENST00000663739.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

Genes affected

(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 = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663739.1	n.298+39415T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82231 AN: 151772 Hom.: 22811 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.509

GnomAD3 exomes AF: 0.470 AC: 44911 AN: 95468 Hom.: 10949 AF XY: 0.478 AC XY: 25212 AN XY: 52710

Gnomad AFR exome AF: 0.644

Gnomad AMR exome AF: 0.387

Gnomad ASJ exome AF: 0.360

Gnomad EAS exome AF: 0.529

Gnomad SAS exome AF: 0.550

Gnomad FIN exome AF: 0.432

Gnomad NFE exome AF: 0.466

Gnomad OTH exome AF: 0.430

GnomAD4 exome AF: 0.499 AC: 129320 AN: 258970 Hom.: 33243 Cov.: 0 AF XY: 0.508 AC XY: 76156 AN XY: 149936

Gnomad4 AFR exome AF: 0.636

Gnomad4 AMR exome AF: 0.391

Gnomad4 ASJ exome AF: 0.360

Gnomad4 EAS exome AF: 0.533

Gnomad4 SAS exome AF: 0.580

Gnomad4 FIN exome AF: 0.457

Gnomad4 NFE exome AF: 0.491

Gnomad4 OTH exome AF: 0.485

GnomAD4 genome AF: 0.542 AC: 82343 AN: 151890 Hom.: 22862 Cov.: 31 AF XY: 0.538 AC XY: 39900 AN XY: 74222

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.511

Alfa AF: 0.499 Hom.: 3680

Bravo AF: 0.548

Asia WGS AF: 0.561 AC: 1953 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	0.67
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2639486; hg19: chr13-83597934;