rs2274598

Positions:

• chr9-114657852-A-G

Variant summary

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

The ENST00000415101.1(TEX53):​n.101-1245T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 398,136 control chromosomes in the GnomAD database, including 874 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 0.030 (126 hom., cov: 32)
  • Exomes 𝑓: 0.050 (748 hom.)
• Consequence: TEX53 ENST00000415101.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

Genes affected

TEX53 (HGNC:53655): (testis expressed 53)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX53	NM_001354645.2			upstream_gene_variant		ENST00000423632.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX53	ENST00000415101.1	n.101-1245T>C		intron_variant, non_coding_transcript_variant		3
TEX53	ENST00000423632.3			upstream_gene_variant		2	NM_001354645.2	P1

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4527 AN: 152156 Hom.: 127 Cov.: 32

Gnomad AFR AF: 0.00683

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0941

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0253

GnomAD4 exome AF: 0.0503 AC: 12369 AN: 245862 Hom.: 748 Cov.: 0 AF XY: 0.0491 AC XY: 6119 AN XY: 124610

Gnomad4 AFR exome AF: 0.00711

Gnomad4 AMR exome AF: 0.0225

Gnomad4 ASJ exome AF: 0.0457

Gnomad4 EAS exome AF: 0.218

Gnomad4 SAS exome AF: 0.0165

Gnomad4 FIN exome AF: 0.0920

Gnomad4 NFE exome AF: 0.0265

Gnomad4 OTH exome AF: 0.0356

GnomAD4 genome AF: 0.0297 AC: 4530 AN: 152274 Hom.: 126 Cov.: 32 AF XY: 0.0333 AC XY: 2478 AN XY: 74458

Gnomad4 AFR AF: 0.00681

Gnomad4 AMR AF: 0.0227

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0941

Gnomad4 NFE AF: 0.0259

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0281 Hom.: 9

Bravo AF: 0.0249

Asia WGS AF: 0.0830 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2274598; hg19: chr9-117420132;