7-130684806-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052933.4(TSGA13):c.23+382G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,054 control chromosomes in the GnomAD database, including 4,696 homozygotes. 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: 𝑓 0.23 (4696 hom., cov: 32)
• Consequence: TSGA13 NM_052933.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSGA13	NM_052933.4	c.23+382G>A		intron_variant		ENST00000356588.8
TSGA13	NM_001304968.2	c.23+382G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSGA13	ENST00000356588.8	c.23+382G>A		intron_variant		1	NM_052933.4	P1
TSGA13	ENST00000438346.1	c.23+382G>A		intron_variant		5
TSGA13	ENST00000443954.5	c.23+382G>A		intron_variant		4
TSGA13	ENST00000456951.5	c.23+382G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34938 AN: 151936 Hom.: 4698 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.230 AC: 34920 AN: 152054 Hom.: 4696 Cov.: 32 AF XY: 0.229 AC XY: 17046 AN XY: 74308

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.225

Alfa AF: 0.275 Hom.: 9936

Bravo AF: 0.214

Asia WGS AF: 0.231 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.94
Dann	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731699; hg19: chr7-130369644;