22-30181782-A-G

Variant names:

• chr22-30181782-A-G
• rs714027
• XM_011529914.3:c.820-25203A>G

Variant summary

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

The XM_011529914.3(HORMAD2):​c.820-25203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,036 control chromosomes in the GnomAD database, including 16,472 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 0.45 (16472 hom., cov: 32)
• Consequence: HORMAD2 XM_011529914.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 23 publications found

Genes affected

HORMAD2 (HGNC:28383): (HORMA domain containing 2) Predicted to be involved in meiotic sister chromatid cohesion. Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 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: 0.452 AC: 68728 AN: 151918 Hom.: 16482 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.452 AC: 68724 AN: 152036 Hom.: 16472 Cov.: 32 AF XY: 0.446 AC XY: 33174 AN XY: 74318

African (AFR) AF: 0.301 AC: 12474 AN: 41458

American (AMR) AF: 0.402 AC: 6146 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3618 AN: 5162

South Asian (SAS) AF: 0.390 AC: 1880 AN: 4824

European-Finnish (FIN) AF: 0.463 AC: 4891 AN: 10556

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36664 AN: 67974

Other (OTH) AF: 0.445 AC: 940 AN: 2112

Alfa AF: 0.507 Hom.: 55666

Bravo AF: 0.448

Asia WGS AF: 0.490 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.17
DANN	Benign	0.73
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs714027; hg19: chr22-30577771;