rs4731699

Variant names:

• chr7-130684806-C-A
• rs4731699
• NM_052933.4:c.23+382G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-130684806-C-A
• chr7-130684806-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_052933.4(TSGA13):​c.23+382G>T variant causes a intron 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: 32)
• Consequence: TSGA13 NM_052933.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSGA13	NM_052933.4	c.23+382G>T		intron_variant	Intron 2 of 7	ENST00000356588.8	NP_443165.1
TSGA13	NM_001304968.2	c.23+382G>T		intron_variant	Intron 3 of 8		NP_001291897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSGA13	ENST00000356588.8	c.23+382G>T		intron_variant	Intron 2 of 7	1	NM_052933.4	ENSP00000348996.3
TSGA13	ENST00000456951.5	c.23+382G>T		intron_variant	Intron 3 of 8	2		ENSP00000406047.1
TSGA13	ENST00000443954.5	c.23+382G>T		intron_variant	Intron 3 of 5	4		ENSP00000415856.1
TSGA13	ENST00000438346.1	c.23+382G>T		intron_variant	Intron 3 of 4	5		ENSP00000407352.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 22205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.73
DANN	Benign	0.60
PhyloP100		-0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs4731699; hg19: chr7-130369644;