chr11-20597043-C-T

Variant names:

• chr11-20597043-C-T
• rs894747
• ENST00000657767.1:n.-64G>A

Variant summary

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

The ENST00000657767.1(ENSG00000286382):​n.-64G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,984 control chromosomes in the GnomAD database, including 27,792 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 0.60 (27792 hom., cov: 32)
• Consequence: ENSG00000286382 ENST00000657767.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

Genes affected

ENSG00000286382 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.698 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
ENSG00000286382	ENST00000657767.1	n.-64G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90977 AN: 151866 Hom.: 27792 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.599 AC: 90992 AN: 151984 Hom.: 27792 Cov.: 32 AF XY: 0.602 AC XY: 44761 AN XY: 74308

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.639

Alfa AF: 0.646 Hom.: 42592

Bravo AF: 0.588

Asia WGS AF: 0.665 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs894747; hg19: chr11-20618589;