chr10-125591806-C-T

Variant names:

• chr10-125591806-C-T
• rs1368532
• ENST00000532135.5:c.265-14932G>A

Variant summary

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

The ENST00000532135.5(TEX36):​c.265-14932G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,900 control chromosomes in the GnomAD database, including 13,578 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 0.42 (13578 hom., cov: 32)
• Consequence: TEX36 ENST00000532135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 2 publications found

Genes affected

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

TEX36-AS1 (HGNC:49500): (TEX36 antisense RNA 1)

LOC102724793 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX36	NM_001318133.2	c.265-14932G>A		intron_variant	Intron 3 of 3		NP_001305062.1
LOC102724793	XR_428823.2	n.196+6624C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX36	ENST00000532135.5	c.265-14932G>A		intron_variant	Intron 3 of 3	1		ENSP00000431764.1
TEX36-AS1	ENST00000816070.1	n.381+6624C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63515 AN: 151782 Hom.: 13562 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.419 AC: 63581 AN: 151900 Hom.: 13578 Cov.: 32 AF XY: 0.419 AC XY: 31069 AN XY: 74236

African (AFR) AF: 0.452 AC: 18696 AN: 41402

American (AMR) AF: 0.437 AC: 6676 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3466

East Asian (EAS) AF: 0.615 AC: 3163 AN: 5140

South Asian (SAS) AF: 0.337 AC: 1619 AN: 4810

European-Finnish (FIN) AF: 0.426 AC: 4484 AN: 10534

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26329 AN: 67972

Other (OTH) AF: 0.437 AC: 922 AN: 2108

Alfa AF: 0.414 Hom.: 4891

Bravo AF: 0.425

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	2.6
DANN	Benign	0.86
PhyloP100		-0.18
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: rs1368532; hg19: chr10-127280375;