18-13878882-A-G

Variant names:

• chr18-13878882-A-G
• rs11661134

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 0.93 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.930 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

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.909

Alfa AF: 0.934 Hom.: 31914

Bravo AF: 0.925

Asia WGS AF: 0.776 AC: 2700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11661134; hg19: chr18-13878881;