rs4456603

chr18-51284217-G-Achr18-51284217-G-Cchr18-51284217-G-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 0.855 in 151,896 control chromosomes in the GnomAD database, including 56,129 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 0.86 (56129 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.855 AC: 129806 AN: 151778 Hom.: 56102 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.855 AC: 129882 AN: 151896 Hom.: 56129 Cov.: 30 AF XY: 0.851 AC XY: 63180 AN XY: 74224

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.837

Alfa AF: 0.903 Hom.: 84976

Bravo AF: 0.847

Asia WGS AF: 0.848 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.12
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4456603; hg19: chr18-48810587;