rs1038638

Positions:

• chr7-130676252-G-A

Variant summary

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

The NM_052933.4(TSGA13):​c.387+2903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,140 control chromosomes in the GnomAD database, including 16,584 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 0.42 (16584 hom., cov: 33)
• Consequence: TSGA13 NM_052933.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSGA13	NM_052933.4	c.387+2903C>T		intron_variant		ENST00000356588.8
TSGA13	NM_001304968.2	c.387+2903C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSGA13	ENST00000356588.8	c.387+2903C>T		intron_variant		1	NM_052933.4	P1
TSGA13	ENST00000456951.5	c.387+2903C>T		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64389 AN: 152022 Hom.: 16583 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.423 AC: 64393 AN: 152140 Hom.: 16584 Cov.: 33 AF XY: 0.428 AC XY: 31821 AN XY: 74378

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.441

Alfa AF: 0.513 Hom.: 16423

Bravo AF: 0.408

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.45

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: rs1038638; hg19: chr7-130361092;