chr1-231547671-C-A

Variant summary

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

The NM_005999.3(TSNAX):​c.367+5060C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 150,978 control chromosomes in the GnomAD database, including 19,032 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 0.48 ( 19032 hom., cov: 30)

Consequence

TSNAX
NM_005999.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.44
Variant links:
Genes affected
TSNAX (HGNC:12380): (translin associated factor X) This gene encodes a protein which specifically interacts with translin, a DNA-binding protein that binds consensus sequences at breakpoint junctions of chromosomal translocations. The encoded protein contains bipartite nuclear targeting sequences that may provide nuclear transport for translin, which lacks any nuclear targeting motifs. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TSNAXNM_005999.3 linkuse as main transcriptc.367+5060C>A intron_variant ENST00000366639.9 NP_005990.1
TSNAX-DISC1NR_028393.1 linkuse as main transcriptn.525+5060C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSNAXENST00000366639.9 linkuse as main transcriptc.367+5060C>A intron_variant 1 NM_005999.3 ENSP00000355599 P1
TSNAXENST00000413309.3 linkuse as main transcriptc.388+5060C>A intron_variant 3 ENSP00000397537
TSNAXENST00000475168.1 linkuse as main transcriptn.3339+5060C>A intron_variant, non_coding_transcript_variant 2
TSNAXENST00000602825.5 linkuse as main transcriptn.511+5060C>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.479
AC:
72247
AN:
150858
Hom.:
18974
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.708
Gnomad AMI
AF:
0.477
Gnomad AMR
AF:
0.498
Gnomad ASJ
AF:
0.335
Gnomad EAS
AF:
0.538
Gnomad SAS
AF:
0.434
Gnomad FIN
AF:
0.285
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.372
Gnomad OTH
AF:
0.459
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.479
AC:
72371
AN:
150978
Hom.:
19032
Cov.:
30
AF XY:
0.473
AC XY:
34867
AN XY:
73722
show subpopulations
Gnomad4 AFR
AF:
0.708
Gnomad4 AMR
AF:
0.498
Gnomad4 ASJ
AF:
0.335
Gnomad4 EAS
AF:
0.538
Gnomad4 SAS
AF:
0.433
Gnomad4 FIN
AF:
0.285
Gnomad4 NFE
AF:
0.372
Gnomad4 OTH
AF:
0.464
Alfa
AF:
0.416
Hom.:
1717
Bravo
AF:
0.507
Asia WGS
AF:
0.498
AC:
1732
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.080
DANN
Benign
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs1615409; hg19: chr1-231683417; COSMIC: COSV64146048; COSMIC: COSV64146048; API