rs599458

Variant names:

• chr19-20818117-C-T
• rs599458

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0932 in 152,124 control chromosomes in the GnomAD database, including 679 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 0.093 (679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0978 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14157 AN: 152006 Hom.: 678 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0932 AC: 14185 AN: 152124 Hom.: 679 Cov.: 32 AF XY: 0.0933 AC XY: 6943 AN XY: 74382

African (AFR) AF: 0.100 AC: 4165 AN: 41490

American (AMR) AF: 0.0688 AC: 1050 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 238 AN: 3470

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5174

South Asian (SAS) AF: 0.0785 AC: 378 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1228 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0983 AC: 6683 AN: 68000

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0950 Hom.: 118

Bravo AF: 0.0909

Asia WGS AF: 0.0660 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.26
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs599458; hg19: chr19-21000923;