10-125657038-C-T

Variant names:

• chr10-125657038-C-T
• rs9422913
• NM_001128202.3:c.265-842G>A

Variant summary

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

The NM_001128202.3(TEX36):​c.265-842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,772 control chromosomes in the GnomAD database, including 10,772 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 0.30 (10772 hom., cov: 32)
• Consequence: TEX36 NM_001128202.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601

Genes affected

TEX36 (HGNC:31653): (testis expressed 36)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX36	NM_001128202.3	c.265-842G>A		intron_variant	Intron 3 of 3	ENST00000368821.4	NP_001121674.1
TEX36	NM_001318133.2	c.264+3983G>A		intron_variant	Intron 3 of 3		NP_001305062.1
TEX36	XM_005269817.5	c.264+3983G>A		intron_variant	Intron 3 of 3		XP_005269874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX36	ENST00000368821.4	c.265-842G>A		intron_variant	Intron 3 of 3	1	NM_001128202.3	ENSP00000357811.3
TEX36	ENST00000532135.5	c.264+3983G>A		intron_variant	Intron 3 of 3	1		ENSP00000431764.1
TEX36	ENST00000526819.5	c.264+3983G>A		intron_variant	Intron 3 of 3	5		ENSP00000434299.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44808 AN: 151654 Hom.: 10722 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.296 AC: 44925 AN: 151772 Hom.: 10772 Cov.: 32 AF XY: 0.296 AC XY: 21936 AN XY: 74202

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.0841

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.273

Alfa AF: 0.138 Hom.: 3832

Bravo AF: 0.334

Asia WGS AF: 0.368 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.51

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: rs9422913; hg19: chr10-127345607;