rs9625921

Variant names:

• chr22-30112286-C-G
• rs9625921
• NM_152510.4:c.316-210C>G

Variant summary

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

The NM_152510.4(HORMAD2):​c.316-210C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,774 control chromosomes in the GnomAD database, including 16,128 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 (16128 hom., cov: 31)
• Consequence: HORMAD2 NM_152510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 12 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HORMAD2	NM_152510.4	c.316-210C>G		intron_variant	Intron 6 of 10	ENST00000336726.11	NP_689723.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HORMAD2	ENST00000336726.11	c.316-210C>G		intron_variant	Intron 6 of 10	1	NM_152510.4	ENSP00000336984.6
HORMAD2	ENST00000403975.1	c.316-210C>G		intron_variant	Intron 6 of 10	2		ENSP00000385055.1
HORMAD2	ENST00000450612.5	n.*3-210C>G		intron_variant	Intron 5 of 8	5		ENSP00000393415.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67794 AN: 151654 Hom.: 16097 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.447 AC: 67888 AN: 151774 Hom.: 16128 Cov.: 31 AF XY: 0.450 AC XY: 33378 AN XY: 74188

African (AFR) AF: 0.603 AC: 24975 AN: 41410

American (AMR) AF: 0.478 AC: 7294 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5166

South Asian (SAS) AF: 0.482 AC: 2317 AN: 4808

European-Finnish (FIN) AF: 0.423 AC: 4457 AN: 10526

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24785 AN: 67826

Other (OTH) AF: 0.451 AC: 951 AN: 2108

Alfa AF: 0.412 Hom.: 1679

Bravo AF: 0.452

Asia WGS AF: 0.412 AC: 1417 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.39
PhyloP100		0.022
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9625921; hg19: chr22-30508275;