20-5113878-G-C

Variant names:

• chr20-5113878-G-C
• rs3730453
• ENST00000516558.1:n.*115C>G

Variant summary

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

The ENST00000516558.1(Y_RNA):​n.*115C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,380 control chromosomes in the GnomAD database, including 2,586 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 0.16 (2586 hom., cov: 33)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: Y_RNA ENST00000516558.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

Y_RNA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 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
Y_RNA	ENST00000516558.1	n.*115C>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23586 AN: 151256 Hom.: 2580 Cov.: 33

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000777

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.156 AC: 23619 AN: 151372 Hom.: 2586 Cov.: 33 AF XY: 0.153 AC XY: 11276 AN XY: 73894

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.000779

Gnomad4 SAS AF: 0.0587

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.153

Alfa AF: 0.127 Hom.: 221

Bravo AF: 0.165

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.16
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3730453; hg19: chr20-5094524;