chr15-56395161-C-A

Position:

• chr15-56395161-C-A

Variant summary

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

The NM_001395496.1(TEX9):​c.828+327C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 302,150 control chromosomes in the GnomAD database, including 26,890 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 (13474 hom., cov: 32)
  • Exomes 𝑓: 0.42 (13416 hom.)
• Consequence: TEX9 NM_001395496.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

TEX9 (HGNC:29585): (testis expressed 9)

ENSG00000259941 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX9	NM_001395496.1	c.828+327C>A		intron_variant		ENST00000696102.1	NP_001382425.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX9	ENST00000696102.1	c.828+327C>A		intron_variant			NM_001395496.1	ENSP00000512397.1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63473 AN: 151714 Hom.: 13472 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.393

GnomAD4 exome AF: 0.418 AC: 62820 AN: 150318 Hom.: 13416 Cov.: 0 AF XY: 0.416 AC XY: 31386 AN XY: 75368

Gnomad4 AFR exome AF: 0.396

Gnomad4 AMR exome AF: 0.405

Gnomad4 ASJ exome AF: 0.362

Gnomad4 EAS exome AF: 0.289

Gnomad4 SAS exome AF: 0.301

Gnomad4 FIN exome AF: 0.443

Gnomad4 NFE exome AF: 0.442

Gnomad4 OTH exome AF: 0.419

GnomAD4 genome AF: 0.418 AC: 63503 AN: 151832 Hom.: 13474 Cov.: 32 AF XY: 0.415 AC XY: 30801 AN XY: 74194

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.390

Alfa AF: 0.339 Hom.: 1267

Bravo AF: 0.415

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6493856; hg19: chr15-56687359;