chr7-130679195-G-A

Variant names:

• chr7-130679195-G-A
• rs782139719
• NM_052933.4:c.347C>T

Variant summary

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

The NM_052933.4(TSGA13):​c.347C>T​(p.Ala116Val) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A116E) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TSGA13 NM_052933.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 1 publications found

Genes affected

TSGA13 (HGNC:12369): (testis specific 13)

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=0.08072671).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSGA13	NM_052933.4	c.347C>T	p.Ala116Val	missense_variant	Exon 5 of 8	ENST00000356588.8	NP_443165.1
TSGA13	NM_001304968.2	c.347C>T	p.Ala116Val	missense_variant	Exon 6 of 9		NP_001291897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSGA13	ENST00000356588.8	c.347C>T	p.Ala116Val	missense_variant	Exon 5 of 8	1	NM_052933.4	ENSP00000348996.3
TSGA13	ENST00000456951.5	c.347C>T	p.Ala116Val	missense_variant	Exon 6 of 9	2		ENSP00000406047.1
TSGA13	ENST00000443954.5	c.*118C>T		downstream_gene_variant		4		ENSP00000415856.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	11
DANN	Uncertain	1.0
DEOGEN2	Benign	0.077	T;T
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.82
FATHMM_MKL	Benign	0.053	N
LIST_S2	Benign	0.51	.;T
M_CAP	Benign	0.0033	T
MetaRNN	Benign	0.081	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.3	L;L
PhyloP100		1.3
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-2.1	N;N
REVEL	Benign	0.082
Sift	Benign	0.056	T;T
Sift4G	Benign	0.17	T;T
Polyphen		0.39	B;B
Vest4		0.16
MutPred		0.074		Loss of ubiquitination at K118 (P = 0.0433);Loss of ubiquitination at K118 (P = 0.0433);
MVP		0.030
MPC		0.36
ClinPred		0.25	T
GERP RS		2.9
Varity_R		0.049
gMVP		0.041
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs782139719; hg19: chr7-130364033;