22-46146500-G-A

Position:

• chr22-46146500-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.0017 (0 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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: 0.00 AC: 166 AN: 99068 Hom.: 0 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.000599

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000650

Gnomad ASJ AF: 0.000818

Gnomad EAS AF: 0.00129

Gnomad SAS AF: 0.000600

Gnomad FIN AF: 0.000816

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00299

Gnomad OTH AF: 0.00145

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00167 AC: 166 AN: 99158 Hom.: 0 Cov.: 28 AF XY: 0.00153 AC XY: 74 AN XY: 48472

Gnomad4 AFR AF: 0.000597

Gnomad4 AMR AF: 0.000649

Gnomad4 ASJ AF: 0.000818

Gnomad4 EAS AF: 0.00129

Gnomad4 SAS AF: 0.000601

Gnomad4 FIN AF: 0.000816

Gnomad4 NFE AF: 0.00299

Gnomad4 OTH AF: 0.00143

Alfa AF: 0.0375 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3885584; hg19: chr22-46542403;