rs4456603

Variant names:

• chr18-51284217-G-A
• rs4456603

Your query was ambiguous. Multiple possible variants found:

• chr18-51284217-G-A
• chr18-51284217-G-C
• chr18-51284217-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;