9-114657852-A-T

Variant names:

• chr9-114657852-A-T
• rs2274598
• ENST00000415101.1:n.101-1245T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000415101.1(TEX53):​n.101-1245T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000407 in 245,876 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: TEX53 ENST00000415101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 0 publications found

Genes affected

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

ENSG00000294099 (HGNC:):

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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415101.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX53	NM_001354645.2	MANE Select	c.-78T>A		upstream_gene	N/A	NP_001341574.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX53	ENST00000415101.1	TSL:3	n.101-1245T>A		intron	N/A
	TEX53	ENST00000423632.3	TSL:2 MANE Select	c.-78T>A		upstream_gene	N/A	ENSP00000489944.1
	ENSG00000294099	ENST00000720956.1		n.-24A>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000407 AC: 1 AN: 245876 Hom.: 0 Cov.: 0 AF XY: 0.00000802 AC XY: 1 AN XY: 124616

African (AFR) AF: 0.00 AC: 0 AN: 7172

American (AMR) AF: 0.00 AC: 0 AN: 7424

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9228

East Asian (EAS) AF: 0.00 AC: 0 AN: 22864

South Asian (SAS) AF: 0.00 AC: 0 AN: 2962

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20778

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1292

European-Non Finnish (NFE) AF: 0.00000634 AC: 1 AN: 157808

Other (OTH) AF: 0.00 AC: 0 AN: 16348

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.78
PhyloP100		-0.47
PromoterAI		0.0075	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2274598; hg19: chr9-117420132;