rs12023718

Variant summary

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

The ENST00000367639.1(TEX35):​c.611-558T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 889,078 control chromosomes in the GnomAD database, including 7,611 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 0.14 ( 1818 hom., cov: 32)
Exomes 𝑓: 0.12 ( 5793 hom. )

Consequence

TEX35
ENST00000367639.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308
Variant links:
Genes affected
TEX35 (HGNC:25366): (testis expressed 35) Located in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TEX35NM_001170722.2 linkuse as main transcriptc.611-558T>C intron_variant NP_001164193.1
TEX35NM_001170724.2 linkuse as main transcriptc.587-558T>C intron_variant NP_001164195.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TEX35ENST00000367639.1 linkuse as main transcriptc.611-558T>C intron_variant 1 ENSP00000356611 Q5T0J7-2
TEX35ENST00000419909.6 linkuse as main transcriptc.*341+1480T>C intron_variant, NMD_transcript_variant 2 ENSP00000430720

Frequencies

GnomAD3 genomes
AF:
0.142
AC:
21625
AN:
152034
Hom.:
1802
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.234
Gnomad AMI
AF:
0.128
Gnomad AMR
AF:
0.104
Gnomad ASJ
AF:
0.136
Gnomad EAS
AF:
0.100
Gnomad SAS
AF:
0.105
Gnomad FIN
AF:
0.0628
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.113
Gnomad OTH
AF:
0.143
GnomAD4 exome
AF:
0.122
AC:
89742
AN:
736926
Hom.:
5793
AF XY:
0.122
AC XY:
42321
AN XY:
347932
show subpopulations
Gnomad4 AFR exome
AF:
0.239
Gnomad4 AMR exome
AF:
0.0837
Gnomad4 ASJ exome
AF:
0.134
Gnomad4 EAS exome
AF:
0.0996
Gnomad4 SAS exome
AF:
0.0923
Gnomad4 FIN exome
AF:
0.0652
Gnomad4 NFE exome
AF:
0.121
Gnomad4 OTH exome
AF:
0.122
GnomAD4 genome
AF:
0.142
AC:
21680
AN:
152152
Hom.:
1818
Cov.:
32
AF XY:
0.137
AC XY:
10209
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.235
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.136
Gnomad4 EAS
AF:
0.100
Gnomad4 SAS
AF:
0.104
Gnomad4 FIN
AF:
0.0628
Gnomad4 NFE
AF:
0.113
Gnomad4 OTH
AF:
0.148
Alfa
AF:
0.121
Hom.:
386
Bravo
AF:
0.149
Asia WGS
AF:
0.149
AC:
518
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
3.6
DANN
Benign
0.42

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: rs12023718; hg19: chr1-178491879; API