rs603097

Variant names:

• chr18-54226736-G-A
• rs603097

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 0.846 in 152,082 control chromosomes in the GnomAD database, including 54,871 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 0.85 (54871 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.846 AC: 128514 AN: 151964 Hom.: 54811 Cov.: 30

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.846 AC: 128634 AN: 152082 Hom.: 54871 Cov.: 30 AF XY: 0.848 AC XY: 62995 AN XY: 74328

African (AFR) AF: 0.956 AC: 39730 AN: 41540

American (AMR) AF: 0.796 AC: 12159 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2895 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5162 AN: 5180

South Asian (SAS) AF: 0.779 AC: 3752 AN: 4818

European-Finnish (FIN) AF: 0.823 AC: 8641 AN: 10500

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53535 AN: 67980

Other (OTH) AF: 0.840 AC: 1772 AN: 2110

Alfa AF: 0.796 Hom.: 23552

Bravo AF: 0.848

Asia WGS AF: 0.904 AC: 3145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs603097; hg19: chr18-51753106;