NM_001170698.2:c.160C>G

Variant names:

• chr17-3467438-G-C
• NM_001170698.2:c.160C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001170698.2(SPATA22):​c.160C>G​(p.Pro54Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,445,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: SPATA22 NM_001170698.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

Genes affected

SPATA22 (HGNC:30705): (spermatogenesis associated 22) Predicted to be involved in regulation of meiotic cell cycle. Predicted to act upstream of or within several processes, including fertilization; gamete generation; and meiosis I cell cycle process. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13379017).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA22	NM_001170698.2	c.160C>G	p.Pro54Ala	missense_variant	Exon 3 of 9	ENST00000572969.6	NP_001164169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA22	ENST00000572969.6	c.160C>G	p.Pro54Ala	missense_variant	Exon 3 of 9	1	NM_001170698.2	ENSP00000460187.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.92e-7 AC: 1 AN: 1445306 Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1 AN XY: 718106

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000123

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.91
DEOGEN2	Benign	0.026	T;T;T;T;.;T
Eigen	Benign	-0.20
Eigen_PC	Benign	-0.13
FATHMM_MKL	Benign	0.72	D
LIST_S2	Benign	0.68	.;.;.;T;T;T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.13	T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.1	M;M;M;M;M;.
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.2	N;.;.;.;N;.
REVEL	Benign	0.054
Sift	Uncertain	0.025	D;.;.;.;D;.
Sift4G	Uncertain	0.060	T;T;T;T;D;T
Polyphen		0.70	P;P;P;P;.;.
Vest4		0.40
MutPred		0.26		Loss of catalytic residue at P53 (P = 0.0103);Loss of catalytic residue at P53 (P = 0.0103);Loss of catalytic residue at P53 (P = 0.0103);Loss of catalytic residue at P53 (P = 0.0103);Loss of catalytic residue at P53 (P = 0.0103);Loss of catalytic residue at P53 (P = 0.0103);
MVP		0.085
MPC		0.098
ClinPred		0.35	T
GERP RS		3.3
Varity_R		0.046
gMVP		0.18

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-3370732;