13-82890356-C-T

Position:

• chr13-82890356-C-T

Variant summary

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

The ENST00000663739.1(ENSG00000286385):​n.299-111752G>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 0.833 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: ENST00000663739.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663739.1	n.299-111752G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.847

Alfa AF: 0.872 Hom.: 26465

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466618; hg19: chr13-83464491;