18-22504711-T-G

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 0.822 in 152,112 control chromosomes in the GnomAD database, including 51,578 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 0.82 (51578 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 125000 AN: 151994 Hom.: 51540 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.822 AC: 125091 AN: 152112 Hom.: 51578 Cov.: 31 AF XY: 0.823 AC XY: 61219 AN XY: 74358

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.831

Alfa AF: 0.829 Hom.: 7006

Bravo AF: 0.812

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.86
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs473518; hg19: chr18-20084674;