chr13-82890356-C-T

Variant names:

• chr13-82890356-C-T
• rs1466618
• ENST00000663739.1:n.299-111752G>A

Variant summary

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

The ENST00000663739.1(ENSG00000286385):​n.299-111752G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,132 control chromosomes in the GnomAD database, including 53,551 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 0.83 (53551 hom., cov: 33)
• Consequence: ENSG00000286385 ENST00000663739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.32
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286385	ENST00000663739.1	n.299-111752G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126599 AN: 152014 Hom.: 53516 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.833 AC: 126684 AN: 152132 Hom.: 53551 Cov.: 33 AF XY: 0.834 AC XY: 62073 AN XY: 74384

African (AFR) AF: 0.679 AC: 28183 AN: 41482

American (AMR) AF: 0.880 AC: 13448 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3214 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4469 AN: 5180

South Asian (SAS) AF: 0.772 AC: 3723 AN: 4824

European-Finnish (FIN) AF: 0.927 AC: 9837 AN: 10612

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60926 AN: 67970

Other (OTH) AF: 0.847 AC: 1788 AN: 2110

Alfa AF: 0.872 Hom.: 29743

Bravo AF: 0.825

Asia WGS AF: 0.824 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.035
DANN	Benign	0.59
PhyloP100		-5.3

Splicing

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

Other links and lift over

dbSNP: rs1466618; hg19: chr13-83464491;