NM_025244.4:c.2060G>T

Variant names:

• chr2-99018212-C-A
• rs148460657
• NM_025244.4:c.2060G>T

Variant summary

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

The NM_025244.4(TSGA10):​c.2060G>T​(p.Arg687Leu) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TSGA10 NM_025244.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

TSGA10 (HGNC:14927): (testis specific 10) Predicted to enable structural molecule activity. Predicted to be involved in spermatogenesis. Predicted to act upstream of or within cell projection assembly. Predicted to be located in neuron projection; sperm fibrous sheath; and sperm principal piece. Implicated in spermatogenic failure 26. [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=0.23386955).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSGA10	NM_025244.4	c.2060G>T	p.Arg687Leu	missense_variant	Exon 20 of 21	ENST00000393483.8	NP_079520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSGA10	ENST00000393483.8	c.2060G>T	p.Arg687Leu	missense_variant	Exon 20 of 21	1	NM_025244.4	ENSP00000377123.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Uncertain	0.012	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.043	T;T;T;T;.
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.45
FATHMM_MKL	Benign	0.72	D
LIST_S2	Uncertain	0.89	.;.;D;D;D
M_CAP	Benign	0.041	D
MetaRNN	Benign	0.23	T;T;T;T;T
MetaSVM	Benign	-0.86	T
MutationAssessor	Benign	1.0	L;L;L;.;.
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-2.1	N;N;N;N;N
REVEL	Benign	0.18
Sift	Uncertain	0.0080	D;D;D;D;D
Sift4G	Uncertain	0.055	T;T;T;.;.
Polyphen		0.99	D;D;D;.;.
Vest4		0.67
MVP		0.35
MPC		0.38
ClinPred		0.92	D
GERP RS		5.0
Varity_R		0.12
gMVP		0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs148460657; hg19: chr2-99634675;