20-5013816-G-T

Variant names:

• chr20-5013816-G-T
• rs6053034
• ENST00000435457.1:n.-92C>A

Variant summary

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

The ENST00000435457.1(ENSG00000234573):​n.-92C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,032 control chromosomes in the GnomAD database, including 8,259 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 0.27 (8259 hom., cov: 31)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: ENSG00000234573 ENST00000435457.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

ENSG00000234573 (HGNC:35577):

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 (AFR) allele frequency at 95% confidence interval = 0.561 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
ENSG00000234573	ENST00000435457.1	n.-92C>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41608 AN: 151802 Hom.: 8242 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.134 AC: 15 AN: 112 Hom.: 0 AF XY: 0.111 AC XY: 10 AN XY: 90

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.250

Gnomad4 NFE exome AF: 0.144

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.274 AC: 41651 AN: 151920 Hom.: 8259 Cov.: 31 AF XY: 0.270 AC XY: 20042 AN XY: 74238

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0156

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.256

Alfa AF: 0.175 Hom.: 1384

Bravo AF: 0.289

Asia WGS AF: 0.117 AC: 406 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	3.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6053034; hg19: chr20-4994462;