TSGA13 p.Lys8Asn

Variant names:

• chr7-130683672-C-A
• NM_052933.4:c.24G>T
• TSGA13 p.Lys8Asn

Your query was ambiguous. Multiple possible variants found:

• chr7-130683672-C-A
• chr7-130683672-C-G

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.24G>T​(p.Lys8Asn) variant causes a missense, splice region 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. 15/25 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TSGA13 NM_052933.4 missense, splice_region
• Scores: Splicing: ADA: 0.4076
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 0 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=0.12460017).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052933.4. 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
	TSGA13	NM_052933.4	MANE Select	c.24G>T	p.Lys8Asn	missense splice_region	Exon 3 of 8	NP_443165.1	Q96PP4
	TSGA13	NM_001304968.2		c.24G>T	p.Lys8Asn	missense splice_region	Exon 4 of 9	NP_001291897.1	Q96PP4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSGA13	ENST00000356588.8	TSL:1 MANE Select	c.24G>T	p.Lys8Asn	missense splice_region	Exon 3 of 8	ENSP00000348996.3	Q96PP4
	TSGA13	ENST00000456951.5	TSL:2	c.24G>T	p.Lys8Asn	missense splice_region	Exon 4 of 9	ENSP00000406047.1	Q96PP4
	TSGA13	ENST00000443954.5	TSL:4	c.24G>T	p.Lys8Asn	missense splice_region	Exon 4 of 6	ENSP00000415856.1	C9JIG7

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	17
DANN	Uncertain	1.0
DEOGEN2	Benign	0.25	T
Eigen	Benign	-0.42
Eigen_PC	Benign	-0.38
FATHMM_MKL	Benign	0.15	N
LIST_S2	Benign	0.45	T
M_CAP	Benign	0.0042	T
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.8	L
PhyloP100		0.21
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-2.4	N
REVEL	Benign	0.022
Sift	Uncertain	0.010	D
Sift4G	Uncertain	0.012	D
Varity_R		0.23
gMVP		0.19
Mutation Taster		=75/25	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.41
dbscSNV1_RF	Benign	0.55
SpliceAI score (max)		0.31		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.31		Position offset: 0

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr7-130368510;