10-125655503-T-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001318133.2(TEX36):​c.264+5518A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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>C		intron	N/A	NP_001305062.1	E9PJL2
	TEX36	NM_001128202.3	MANE Select	c.*397A>C		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>C		intron	N/A	ENSP00000431764.1	E9PJL2
	TEX36	ENST00000526819.5	TSL:5	c.264+5518A>C		intron	N/A	ENSP00000434299.1	E9PR91
	TEX36	ENST00000368821.4	TSL:1 MANE Select	c.*397A>C		downstream_gene	N/A	ENSP00000357811.3	Q5VZQ5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.39
PhyloP100		-0.40

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;