22-43917969-A-G

Variant names:

• chr22-43917969-A-G
• rs929090

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.486 in 152,138 control chromosomes in the GnomAD database, including 18,125 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 0.49 (18125 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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: 0.486 AC: 73828 AN: 152020 Hom.: 18100 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.486 AC: 73900 AN: 152138 Hom.: 18125 Cov.: 33 AF XY: 0.492 AC XY: 36611 AN XY: 74390

African (AFR) AF: 0.461 AC: 19133 AN: 41506

American (AMR) AF: 0.539 AC: 8241 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2150 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3203 AN: 5178

South Asian (SAS) AF: 0.525 AC: 2532 AN: 4820

European-Finnish (FIN) AF: 0.526 AC: 5570 AN: 10594

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31393 AN: 67970

Other (OTH) AF: 0.498 AC: 1051 AN: 2110

Alfa AF: 0.474 Hom.: 44414

Bravo AF: 0.487

Asia WGS AF: 0.551 AC: 1914 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs929090; hg19: chr22-44313849;