chr10-125607576-G-T

Variant names:

• chr10-125607576-G-T
• rs9422897
• ENST00000532135.5:c.265-30702C>A

Variant summary

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

The NM_001318133.2(TEX36):​c.265-30702C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 152,140 control chromosomes in the GnomAD database, including 805 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 0.090 (805 hom., cov: 32)
• Consequence: TEX36 NM_001318133.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX36	NM_001318133.2	c.265-30702C>A		intron_variant	Intron 3 of 3		NP_001305062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX36	ENST00000532135.5	c.265-30702C>A		intron_variant	Intron 3 of 3	1		ENSP00000431764.1

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13754 AN: 152022 Hom.: 805 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0904 AC: 13755 AN: 152140 Hom.: 805 Cov.: 32 AF XY: 0.0915 AC XY: 6803 AN XY: 74360

Gnomad4 AFR AF: 0.0310

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.0463

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.110

Alfa AF: 0.111 Hom.: 1279

Bravo AF: 0.0882

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9422897; hg19: chr10-127296145;