rs599019

Variant names:

• chr18-294495-C-A
• rs599019

Your query was ambiguous. Multiple possible variants found:

• chr18-294495-C-A
• chr18-294495-C-G
• chr18-294495-C-T

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 0.777 in 151,844 control chromosomes in the GnomAD database, including 46,173 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 0.78 (46173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 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

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117927 AN: 151726 Hom.: 46124 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.777 AC: 118034 AN: 151844 Hom.: 46173 Cov.: 32 AF XY: 0.778 AC XY: 57749 AN XY: 74246

African (AFR) AF: 0.799 AC: 32916 AN: 41206

American (AMR) AF: 0.818 AC: 12495 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2382 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2953 AN: 5164

South Asian (SAS) AF: 0.850 AC: 4097 AN: 4820

European-Finnish (FIN) AF: 0.783 AC: 8296 AN: 10590

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52504 AN: 67994

Other (OTH) AF: 0.780 AC: 1646 AN: 2110

Alfa AF: 0.777 Hom.: 58511

Bravo AF: 0.779

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.24
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs599019; hg19: chr18-294495;