18-21120994-G-A

Position:

• chr18-21120994-G-A

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 0.804 in 152,046 control chromosomes in the GnomAD database, including 53,163 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 0.80 (53163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601

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 = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122276 AN: 151930 Hom.: 53174 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.804 AC: 122295 AN: 152046 Hom.: 53163 Cov.: 32 AF XY: 0.808 AC XY: 60096 AN XY: 74358

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.977

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.836

Alfa AF: 0.942 Hom.: 23406

Bravo AF: 0.774

Asia WGS AF: 0.895 AC: 3097 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10083915; hg19: chr18-18700955;