22-23888628-G-A

Position:

• chr22-23888628-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 0.764 in 152,108 control chromosomes in the GnomAD database, including 44,634 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 0.76 (44634 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 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: 0.764 AC: 116059 AN: 151990 Hom.: 44578 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.764 AC: 116174 AN: 152108 Hom.: 44634 Cov.: 31 AF XY: 0.768 AC XY: 57107 AN XY: 74346

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.746

Alfa AF: 0.750 Hom.: 6088

Bravo AF: 0.770

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1984309; hg19: chr22-24230815;