rs482360

Variant names:

• chr18-13137993-G-C
• rs482360

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 0.697 in 152,200 control chromosomes in the GnomAD database, including 37,856 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 0.70 (37856 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105937 AN: 152082 Hom.: 37804 Cov.: 34

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.697 AC: 106044 AN: 152200 Hom.: 37856 Cov.: 34 AF XY: 0.698 AC XY: 51928 AN XY: 74398

African (AFR) AF: 0.852 AC: 35410 AN: 41544

American (AMR) AF: 0.667 AC: 10199 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3472

East Asian (EAS) AF: 0.805 AC: 4166 AN: 5176

South Asian (SAS) AF: 0.697 AC: 3361 AN: 4824

European-Finnish (FIN) AF: 0.611 AC: 6470 AN: 10582

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41641 AN: 67988

Other (OTH) AF: 0.705 AC: 1491 AN: 2114

Alfa AF: 0.434 Hom.: 813

Bravo AF: 0.709

Asia WGS AF: 0.799 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs482360; hg19: chr18-13137992;