ENST00000458731.1:n.833A>G

Variant names:

• chr20-56268969-A-G
• rs1326022
• ENST00000458731.1:n.833A>G

Variant summary

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

The ENST00000458731.1(ENSG00000235594):​n.833A>G 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 0.669 in 152,100 control chromosomes in the GnomAD database, including 34,814 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 0.67 (34814 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000235594 ENST00000458731.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

Genes affected

ENSG00000235594 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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
ENSG00000235594	ENST00000458731.1	n.833A>G		non_coding_transcript_exon_variant	Exon 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101787 AN: 151982 Hom.: 34813 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.685

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.669 AC: 101822 AN: 152100 Hom.: 34814 Cov.: 33 AF XY: 0.673 AC XY: 50056 AN XY: 74362

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.684

Alfa AF: 0.699 Hom.: 25411

Bravo AF: 0.667

Asia WGS AF: 0.798 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
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: rs1326022; hg19: chr20-54844025;