chr10-125655503-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 ENST00000532135.5(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 ENST00000532135.5 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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX36	NM_001318133.2	c.264+5518A>C		intron_variant	Intron 3 of 3		NP_001305062.1
TEX36	XM_005269817.5	c.264+5518A>C		intron_variant	Intron 3 of 3		XP_005269874.1
TEX36	NM_001128202.3	c.*397A>C		downstream_gene_variant		ENST00000368821.4	NP_001121674.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX36	ENST00000532135.5	c.264+5518A>C		intron_variant	Intron 3 of 3	1		ENSP00000431764.1
TEX36	ENST00000526819.5	c.264+5518A>C		intron_variant	Intron 3 of 3	5		ENSP00000434299.1
TEX36	ENST00000368821.4	c.*397A>C		downstream_gene_variant		1	NM_001128202.3	ENSP00000357811.3

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 v4.3

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;