chr18-13878882-A-G

Variant names:

• chr18-13878882-A-G
• rs11661134

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 0.93 in 152,182 control chromosomes in the GnomAD database, including 65,906 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 0.93 (65906 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141354 AN: 152064 Hom.: 65855 Cov.: 30

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.930 AC: 141459 AN: 152182 Hom.: 65906 Cov.: 30 AF XY: 0.929 AC XY: 69158 AN XY: 74408

African (AFR) AF: 0.929 AC: 38560 AN: 41512

American (AMR) AF: 0.931 AC: 14226 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3229 AN: 3472

East Asian (EAS) AF: 0.768 AC: 3973 AN: 5174

South Asian (SAS) AF: 0.817 AC: 3916 AN: 4794

European-Finnish (FIN) AF: 0.985 AC: 10463 AN: 10622

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.943 AC: 64109 AN: 68014

Other (OTH) AF: 0.909 AC: 1916 AN: 2108

Alfa AF: 0.932 Hom.: 55557

Bravo AF: 0.925

Asia WGS AF: 0.776 AC: 2700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.22
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11661134; hg19: chr18-13878881;