rs10900862

Positions:

• chr5-139396890-C-A
• chr5-139396890-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_194296.2(SPATA24):​c.528G>T​(p.Glu176Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SPATA24 NM_194296.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.90

Genes affected

SPATA24 (HGNC:27322): (spermatogenesis associated 24) Predicted to enable DNA binding activity and identical protein binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.29880795).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA24	NM_194296.2	c.528G>T	p.Glu176Asp	missense_variant	6/6	ENST00000450845.7	NP_919272.1
SPATA24	XM_005271916.5	c.554G>T	p.Arg185Ile	missense_variant	6/6		XP_005271973.1
SPATA24	XM_011543252.3	c.437G>T	p.Arg146Ile	missense_variant	6/6		XP_011541554.1
SPATA24	XM_011543253.3	c.437G>T	p.Arg146Ile	missense_variant	6/6		XP_011541555.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA24	ENST00000450845.7	c.528G>T	p.Glu176Asp	missense_variant	6/6	1	NM_194296.2	ENSP00000414920.2
SPATA24	ENST00000302091.9	c.554G>T	p.Arg185Ile	missense_variant	6/6	2		ENSP00000302917.5
SPATA24	ENST00000512761.5	c.372G>T	p.Glu124Asp	missense_variant	5/5	5		ENSP00000426748.1
SPATA24	ENST00000514983.5	c.413G>T	p.Arg138Ile	missense_variant	5/5	5		ENSP00000423424.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 67

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Uncertain	0.083	D
BayesDel_noAF	Benign	-0.12
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0050	T;T
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.66	T;T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.30	T;T
MetaSVM	Benign	-0.71	T
MutationAssessor	Benign	0.34	N;.
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-1.8	N;N
REVEL	Benign	0.23
Sift	Benign	0.12	T;T
Sift4G	Benign	0.27	T;T
Polyphen		0.99	D;.
Vest4		0.43
MutPred		0.088		Loss of methylation at K173 (P = 0.0864);.;
MVP		0.030
ClinPred		0.96	D
GERP RS		5.7
Varity_R		0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10900862; hg19: chr5-138732579;