13-83023799-A-T

Variant names:

• chr13-83023799-A-T
• rs2639486
• ENST00000663739.1:n.298+39415T>A

Variant summary

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

The ENST00000663739.1(ENSG00000286385):​n.298+39415T>A variant causes a intron 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: ENSG00000286385 ENST00000663739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 2 publications found

Genes affected

ENSG00000286385 (HGNC:):

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 = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663739.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286385	ENST00000663739.1		n.298+39415T>A		intron	N/A

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

GnomAD2 exomes AF: 0.470 AC: 44911 AN: 95468 AF XY: 0.478

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 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

African (AFR) AF: 0.636 AC: 3390 AN: 5334

American (AMR) AF: 0.391 AC: 6785 AN: 17336

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 3220 AN: 8936

East Asian (EAS) AF: 0.533 AC: 3916 AN: 7352

South Asian (SAS) AF: 0.580 AC: 29738 AN: 51304

European-Finnish (FIN) AF: 0.457 AC: 5393 AN: 11796

Middle Eastern (MID) AF: 0.398 AC: 452 AN: 1136

European-Non Finnish (NFE) AF: 0.491 AC: 70549 AN: 143650

Other (OTH) AF: 0.485 AC: 5877 AN: 12126

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

African (AFR) AF: 0.677 AC: 28042 AN: 41400

American (AMR) AF: 0.466 AC: 7113 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2867 AN: 5148

South Asian (SAS) AF: 0.596 AC: 2870 AN: 4818

European-Finnish (FIN) AF: 0.439 AC: 4626 AN: 10534

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33910 AN: 67946

Other (OTH) AF: 0.511 AC: 1077 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.43
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2639486; hg19: chr13-83597934;