rs146859197

Variant names:

• chr11-133842061-C-A
• rs146859197
• NM_174927.3:c.482G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-133842061-C-A
• chr11-133842061-C-G
• chr11-133842061-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_174927.3(SPATA19):​c.482G>T​(p.Arg161Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R161T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SPATA19 NM_174927.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 0 publications found

Genes affected

SPATA19 (HGNC:30614): (spermatogenesis associated 19) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23784515).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174927.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA19	NM_174927.3	MANE Select	c.482G>T	p.Arg161Ile	missense	Exon 6 of 7	NP_777587.1	A0A140VKB6
	SPATA19	NM_001291992.2		c.482G>T	p.Arg161Ile	missense	Exon 6 of 7	NP_001278921.1	A0A140VKB6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA19	ENST00000299140.8	TSL:1 MANE Select	c.482G>T	p.Arg161Ile	missense	Exon 6 of 7	ENSP00000299140.3	Q7Z5L4
	SPATA19	ENST00000532889.1	TSL:5	c.482G>T	p.Arg161Ile	missense	Exon 6 of 7	ENSP00000435248.1	Q7Z5L4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251388 AF XY: 0.00000736

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.090	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.96
DEOGEN2	Benign	0.084	T
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.87
FATHMM_MKL	Benign	0.027	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.035	D
MetaRNN	Benign	0.24	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.5	L
PhyloP100		-0.27
PrimateAI	Benign	0.29	T
PROVEAN	Uncertain	-3.7	D
REVEL	Benign	0.090
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.011	D
Polyphen		0.81	P
Vest4		0.50
MutPred		0.20		Loss of glycosylation at P162 (P = 0.0577)
MVP		0.16
MPC		0.23
ClinPred		0.94	D
GERP RS		0.76
Varity_R		0.24
gMVP		0.045
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs146859197; hg19: chr11-133711956;