rs4810113

chr20-58002043-G-A

Variant summary

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

The variant allele was found at a frequency of 0.118 in 152,248 control chromosomes in the GnomAD database, including 1,388 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 0.12 (1388 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18007 AN: 152128 Hom.: 1385 Cov.: 32

Gnomad AFR AF: 0.0271

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.118 AC: 18019 AN: 152248 Hom.: 1388 Cov.: 32 AF XY: 0.124 AC XY: 9224 AN XY: 74446

Gnomad4 AFR AF: 0.0271

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.122

Alfa AF: 0.139 Hom.: 1604

Bravo AF: 0.114

Asia WGS AF: 0.147 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.0010
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4810113; hg19: chr20-56577099;