22-43109689-A-G

Variant names:

• chr22-43109689-A-G
• rs4988366

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 0.179 in 152,152 control chromosomes in the GnomAD database, including 2,912 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 0.18 (2912 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27223 AN: 152034 Hom.: 2914 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.179 AC: 27243 AN: 152152 Hom.: 2912 Cov.: 33 AF XY: 0.176 AC XY: 13073 AN XY: 74378

African (AFR) AF: 0.295 AC: 12228 AN: 41468

American (AMR) AF: 0.202 AC: 3079 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3472

East Asian (EAS) AF: 0.0556 AC: 288 AN: 5180

South Asian (SAS) AF: 0.130 AC: 629 AN: 4826

European-Finnish (FIN) AF: 0.0991 AC: 1051 AN: 10608

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8758 AN: 68002

Other (OTH) AF: 0.184 AC: 390 AN: 2116

Alfa AF: 0.128 Hom.: 1577

Bravo AF: 0.189

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4988366; hg19: chr22-43505695;