rs1025526

Variant summary

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

The NR_028393.1(TSNAX-DISC1):​n.526-1749C>T 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 0.544 in 152,120 control chromosomes in the GnomAD database, including 24,208 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 0.54 ( 24208 hom., cov: 33)

Consequence

TSNAX-DISC1
NR_028393.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.462
Variant links:
Genes affected

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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TSNAX-DISC1NR_028393.1 linkuse as main transcriptn.526-1749C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.544
AC:
82749
AN:
152002
Hom.:
24199
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.359
Gnomad AMI
AF:
0.760
Gnomad AMR
AF:
0.522
Gnomad ASJ
AF:
0.629
Gnomad EAS
AF:
0.185
Gnomad SAS
AF:
0.576
Gnomad FIN
AF:
0.624
Gnomad MID
AF:
0.713
Gnomad NFE
AF:
0.665
Gnomad OTH
AF:
0.588
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.544
AC:
82777
AN:
152120
Hom.:
24208
Cov.:
33
AF XY:
0.540
AC XY:
40130
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.359
Gnomad4 AMR
AF:
0.522
Gnomad4 ASJ
AF:
0.629
Gnomad4 EAS
AF:
0.186
Gnomad4 SAS
AF:
0.576
Gnomad4 FIN
AF:
0.624
Gnomad4 NFE
AF:
0.665
Gnomad4 OTH
AF:
0.584
Alfa
AF:
0.600
Hom.:
3517
Bravo
AF:
0.525
Asia WGS
AF:
0.413
AC:
1433
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.7
DANN
Benign
0.58

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: rs1025526; hg19: chr1-231750641; COSMIC: COSV71449416; API