5-139396890-C-T

Variant names:

• chr5-139396890-C-T
• rs10900862
• NM_194296.2:c.528G>A

Variant summary

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

The NM_194296.2(SPATA24):​c.528G>A​(p.Glu176Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.624 in 1,551,496 control chromosomes in the GnomAD database, including 314,613 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 0.50 (22364 hom., cov: 32)
  • Exomes 𝑓: 0.64 (292249 hom.)
• Consequence: SPATA24 NM_194296.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.90
• Publications: 26 publications found

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]

ENSG00000302512 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=9.923242E-6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194296.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA24	NM_194296.2	MANE Select	c.528G>A	p.Glu176Glu	synonymous	Exon 6 of 6	NP_919272.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA24	ENST00000450845.7	TSL:1 MANE Select	c.528G>A	p.Glu176Glu	synonymous	Exon 6 of 6	ENSP00000414920.2
	SPATA24	ENST00000302091.9	TSL:2	c.554G>A	p.Arg185Lys	missense	Exon 6 of 6	ENSP00000302917.5
	SPATA24	ENST00000514983.5	TSL:5	c.413G>A	p.Arg138Lys	missense	Exon 5 of 5	ENSP00000423424.1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75531 AN: 151992 Hom.: 22372 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.510

GnomAD2 exomes AF: 0.584 AC: 91392 AN: 156548 AF XY: 0.586

Gnomad AFR exome AF: 0.158

Gnomad AMR exome AF: 0.624

Gnomad ASJ exome AF: 0.537

Gnomad EAS exome AF: 0.297

Gnomad FIN exome AF: 0.700

Gnomad NFE exome AF: 0.660

Gnomad OTH exome AF: 0.585

GnomAD4 exome AF: 0.638 AC: 892645 AN: 1399384 Hom.: 292249 Cov.: 67 AF XY: 0.637 AC XY: 439555 AN XY: 690200

African (AFR) AF: 0.161 AC: 5078 AN: 31598

American (AMR) AF: 0.613 AC: 21888 AN: 35704

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 13359 AN: 25182

East Asian (EAS) AF: 0.342 AC: 12234 AN: 35736

South Asian (SAS) AF: 0.553 AC: 43846 AN: 79236

European-Finnish (FIN) AF: 0.690 AC: 33990 AN: 49270

Middle Eastern (MID) AF: 0.529 AC: 3016 AN: 5698

European-Non Finnish (NFE) AF: 0.672 AC: 725536 AN: 1078954

Other (OTH) AF: 0.581 AC: 33698 AN: 58006

GnomAD4 genome AF: 0.496 AC: 75523 AN: 152112 Hom.: 22364 Cov.: 32 AF XY: 0.496 AC XY: 36854 AN XY: 74362

African (AFR) AF: 0.169 AC: 7032 AN: 41516

American (AMR) AF: 0.539 AC: 8224 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1857 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1580 AN: 5164

South Asian (SAS) AF: 0.546 AC: 2630 AN: 4818

European-Finnish (FIN) AF: 0.684 AC: 7245 AN: 10586

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45191 AN: 67978

Other (OTH) AF: 0.506 AC: 1066 AN: 2106

Alfa AF: 0.590 Hom.: 59700

Bravo AF: 0.474

TwinsUK AF: 0.655 AC: 2428

ALSPAC AF: 0.667 AC: 2569

ESP6500AA AF: 0.169 AC: 234

ESP6500EA AF: 0.650 AC: 2067

ExAC AF: 0.526 AC: 12915

Asia WGS AF: 0.398 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Uncertain	0.060
CADD	Benign	9.3
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0040	T
Eigen	Uncertain	0.64
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.35	T
MetaRNN	Benign	0.0000099	T
MetaSVM	Benign	-0.91	T
PhyloP100		3.9
PROVEAN	Benign	0.32	N
REVEL	Benign	0.21
Sift	Benign	0.14	T
Polyphen		1.0	D
ClinPred		0.034	T
GERP RS		5.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10900862; hg19: chr5-138732579; COSMIC: COSV57474341; COSMIC: COSV57474341;