NM_052933.4:c.24G>A

Variant names:

• chr7-130683672-C-T
• rs149851433
• NM_052933.4:c.24G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_052933.4(TSGA13):​c.24G>A​(p.Lys8Lys) variant causes a splice region, synonymous 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. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TSGA13 NM_052933.4 splice_region, synonymous
• Scores: Splicing: ADA: 0.003870
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BP7: Synonymous conserved (PhyloP=0.212 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSGA13	NM_052933.4	c.24G>A	p.Lys8Lys	splice_region_variant, synonymous_variant	Exon 3 of 8	ENST00000356588.8	NP_443165.1
TSGA13	NM_001304968.2	c.24G>A	p.Lys8Lys	splice_region_variant, synonymous_variant	Exon 4 of 9		NP_001291897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSGA13	ENST00000356588.8	c.24G>A	p.Lys8Lys	splice_region_variant, synonymous_variant	Exon 3 of 8	1	NM_052933.4	ENSP00000348996.3
TSGA13	ENST00000456951.5	c.24G>A	p.Lys8Lys	splice_region_variant, synonymous_variant	Exon 4 of 9	2		ENSP00000406047.1
TSGA13	ENST00000443954.5	c.24G>A	p.Lys8Lys	splice_region_variant, synonymous_variant	Exon 4 of 6	4		ENSP00000415856.1
TSGA13	ENST00000438346.1	c.24G>A	p.Lys8Lys	splice_region_variant, synonymous_variant	Exon 4 of 5	5		ENSP00000407352.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		0.21

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0039
dbscSNV1_RF	Benign	0.18
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: rs149851433; hg19: chr7-130368510;