10-125655503-T-C

Variant names:

• chr10-125655503-T-C
• rs10510147
• ENST00000532135.5:c.264+5518A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001318133.2(TEX36):​c.264+5518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 152,302 control chromosomes in the GnomAD database, including 167 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 0.035 (167 hom., cov: 32)
• Consequence: TEX36 NM_001318133.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318133.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX36	NM_001318133.2		c.264+5518A>G		intron	N/A	NP_001305062.1	E9PJL2
	TEX36	NM_001128202.3	MANE Select	c.*397A>G		downstream_gene	N/A	NP_001121674.1	Q5VZQ5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX36	ENST00000532135.5	TSL:1	c.264+5518A>G		intron	N/A	ENSP00000431764.1	E9PJL2
	TEX36	ENST00000526819.5	TSL:5	c.264+5518A>G		intron	N/A	ENSP00000434299.1	E9PR91
	TEX36	ENST00000368821.4	TSL:1 MANE Select	c.*397A>G		downstream_gene	N/A	ENSP00000357811.3	Q5VZQ5

Frequencies

GnomAD3 genomes AF: 0.0347 AC: 5276 AN: 152184 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0347 AC: 5286 AN: 152302 Hom.: 167 Cov.: 32 AF XY: 0.0366 AC XY: 2724 AN XY: 74460

African (AFR) AF: 0.0104 AC: 432 AN: 41570

American (AMR) AF: 0.0397 AC: 607 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.104 AC: 541 AN: 5178

South Asian (SAS) AF: 0.138 AC: 667 AN: 4818

European-Finnish (FIN) AF: 0.0167 AC: 177 AN: 10620

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0371 AC: 2523 AN: 68022

Other (OTH) AF: 0.0412 AC: 87 AN: 2114

Alfa AF: 0.0345 Hom.: 19

Bravo AF: 0.0342

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.48
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10510147; hg19: chr10-127344072;