20-56268969-A-G

Position:

• chr20-56268969-A-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: ENST00000458731.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000458731.1	n.833A>G		non_coding_transcript_exon_variant	2/2

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;