rs360712

Positions:

• chr11-112169304-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_031275.4(TEX12):​c.36A>G​(p.Arg12Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,611,342 control chromosomes in the GnomAD database, including 50,407 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 0.21 (3810 hom., cov: 32)
  • Exomes 𝑓: 0.25 (46597 hom.)
• Consequence: TEX12 NM_031275.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

TEX12 (HGNC:11734): (testis expressed 12) This gene is similar to a mouse gene that is expressed in the testis. [provided by RefSeq, Jul 2008]

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP7: Synonymous conserved (PhyloP=1.47 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX12	NM_031275.4	c.36A>G	p.Arg12Arg	synonymous_variant	2/5	ENST00000280358.5	NP_112565.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX12	ENST00000280358.5	c.36A>G	p.Arg12Arg	synonymous_variant	2/5	1	NM_031275.4	ENSP00000280358.4
ENSG00000255292	ENST00000532699.1	n.315-1115A>G		intron_variant		3		ENSP00000456434.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31419 AN: 152038 Hom.: 3809 Cov.: 32

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.208

GnomAD3 exomes AF: 0.242 AC: 60892 AN: 251194 Hom.: 7872 AF XY: 0.244 AC XY: 33132 AN XY: 135778

Gnomad AFR exome AF: 0.0808

Gnomad AMR exome AF: 0.300

Gnomad ASJ exome AF: 0.243

Gnomad EAS exome AF: 0.133

Gnomad SAS exome AF: 0.225

Gnomad FIN exome AF: 0.280

Gnomad NFE exome AF: 0.263

Gnomad OTH exome AF: 0.251

GnomAD4 exome AF: 0.250 AC: 364210 AN: 1459186 Hom.: 46597 Cov.: 31 AF XY: 0.250 AC XY: 181215 AN XY: 725998

Gnomad4 AFR exome AF: 0.0778

Gnomad4 AMR exome AF: 0.298

Gnomad4 ASJ exome AF: 0.244

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.282

Gnomad4 NFE exome AF: 0.259

Gnomad4 OTH exome AF: 0.237

GnomAD4 genome AF: 0.206 AC: 31410 AN: 152156 Hom.: 3810 Cov.: 32 AF XY: 0.209 AC XY: 15518 AN XY: 74382

Gnomad4 AFR AF: 0.0840

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.205

Alfa AF: 0.245 Hom.: 7997

Bravo AF: 0.200

Asia WGS AF: 0.174 AC: 606 AN: 3478

EpiCase AF: 0.249

EpiControl AF: 0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	11
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs360712; hg19: chr11-112040027; COSMIC: COSV54783543;