rs599458

Positions:

• chr19-20818117-C-T

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 0.0932 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0931 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

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0688

Gnomad4 ASJ AF: 0.0686

Gnomad4 EAS AF: 0.0203

Gnomad4 SAS AF: 0.0785

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0983

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0945 Hom.: 114

Bravo AF: 0.0909

Asia WGS AF: 0.0660 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs599458; hg19: chr19-21000923;