20-52699511-G-A

Position:

• chr20-52699511-G-A

Variant summary

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

The 20-52699511-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,170 control chromosomes in the GnomAD database, including 1,294 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 0.082 (1294 hom., cov: 32)
• Consequence: ENST00000661770.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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
	ENST00000661770.1			downstream_gene_variant
	ENST00000656343.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12466 AN: 152052 Hom.: 1277 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0589

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0613

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

GnomAD4 genome AF: 0.0824 AC: 12534 AN: 152170 Hom.: 1294 Cov.: 32 AF XY: 0.0809 AC XY: 6022 AN XY: 74424

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.0362

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.0241

Gnomad4 NFE AF: 0.0114

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.0315 Hom.: 160

Bravo AF: 0.0895

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.011
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6097080; hg19: chr20-51316050;