rs2274598

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-114657852-A-G
• chr9-114657852-A-T

Variant summary

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

The ENST00000415101.1(TEX53):​n.101-1245T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 2 publications found

Genes affected

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

ENSG00000294099 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TEX53	NM_001354645.2	c.-78T>C		upstream_gene_variant		ENST00000423632.3	NP_001341574.1
LOC107987121	XR_001746908.3	n.-64A>G		upstream_gene_variant
LOC107987121	XR_007061744.1	n.-64A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX53	ENST00000423632.3	c.-78T>C		upstream_gene_variant		2	NM_001354645.2	ENSP00000489944.1

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

African (AFR) AF: 0.00711 AC: 51 AN: 7172

American (AMR) AF: 0.0225 AC: 167 AN: 7424

Ashkenazi Jewish (ASJ) AF: 0.0457 AC: 422 AN: 9228

East Asian (EAS) AF: 0.218 AC: 4989 AN: 22862

South Asian (SAS) AF: 0.0165 AC: 49 AN: 2962

European-Finnish (FIN) AF: 0.0920 AC: 1910 AN: 20770

Middle Eastern (MID) AF: 0.0193 AC: 25 AN: 1292

European-Non Finnish (NFE) AF: 0.0265 AC: 4174 AN: 157804

Other (OTH) AF: 0.0356 AC: 582 AN: 16348

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

African (AFR) AF: 0.00681 AC: 283 AN: 41562

American (AMR) AF: 0.0227 AC: 347 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0426 AC: 148 AN: 3472

East Asian (EAS) AF: 0.131 AC: 680 AN: 5180

South Asian (SAS) AF: 0.0197 AC: 95 AN: 4824

European-Finnish (FIN) AF: 0.0941 AC: 997 AN: 10600

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0259 AC: 1763 AN: 68010

Other (OTH) AF: 0.0274 AC: 58 AN: 2116

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
PhyloP100		-0.47
PromoterAI		0.012	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;