rs10408126
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_052876.4(NACC1):c.-8-46C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,491,228 control chromosomes in the GnomAD database, including 5 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 0.0051 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 3 hom. )
Consequence
NACC1
NM_052876.4 intron
NM_052876.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.79
Genes affected
NACC1 (HGNC:20967): (nucleus accumbens associated 1) This gene encodes a member of the BTB/POZ protein family. BTB/POZ proteins are involved in several cellular processes including proliferation, apoptosis and transcription regulation. The encoded protein is a transcriptional repressor that plays a role in stem cell self-renewal and pluripotency maintenance. The encoded protein also suppresses transcription of the candidate tumor suppressor Gadd45GIP1, and expression of this gene may play a role in the progression of multiple types of cancer. A pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Feb 2012]
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=-0.93).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00512 (780/152318) while in subpopulation AFR AF= 0.018 (748/41570). AF 95% confidence interval is 0.0169. There are 2 homozygotes in gnomad4. There are 380 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 780 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NACC1 | NM_052876.4 | c.-8-46C>T | intron_variant | ENST00000292431.5 | |||
NACC1 | XM_005259721.4 | c.-8-46C>T | intron_variant | ||||
NACC1 | XM_047438118.1 | c.-8-46C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NACC1 | ENST00000292431.5 | c.-8-46C>T | intron_variant | 1 | NM_052876.4 | P1 | |||
NACC1 | ENST00000586171.3 | c.-8-46C>T | intron_variant | 5 | P1 | ||||
NACC1 | ENST00000700232.1 | c.-8-46C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00511 AC: 777AN: 152200Hom.: 2 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
777
AN:
152200
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000536 AC: 717AN: 1338910Hom.: 3 Cov.: 31 AF XY: 0.000490 AC XY: 320AN XY: 653442
GnomAD4 exome
AF:
AC:
717
AN:
1338910
Hom.:
Cov.:
31
AF XY:
AC XY:
320
AN XY:
653442
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00512 AC: 780AN: 152318Hom.: 2 Cov.: 32 AF XY: 0.00510 AC XY: 380AN XY: 74486
GnomAD4 genome
?
AF:
AC:
780
AN:
152318
Hom.:
Cov.:
32
AF XY:
AC XY:
380
AN XY:
74486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
4
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at