rs2274598

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.472
Variant links:
Genes affected
TEX53 (HGNC:53655): (testis expressed 53)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
TEX53NM_001354645.2 linkuse as main transcript upstream_gene_variant ENST00000423632.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEX53ENST00000415101.1 linkuse as main transcriptn.101-1245T>C intron_variant, non_coding_transcript_variant 3
TEX53ENST00000423632.3 linkuse as main transcript upstream_gene_variant 2 NM_001354645.2 P1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2274598; hg19: chr9-117420132; API