11-72002987-G-A

Variant summary

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

The NM_006185.4(NUMA1):​c.*540C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 234,954 control chromosomes in the GnomAD database, including 86 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 0.018 ( 79 hom., cov: 33)
Exomes 𝑓: 0.0050 ( 7 hom. )

Consequence

NUMA1
NM_006185.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.283
Variant links:
Genes affected
NUMA1 (HGNC:8059): (nuclear mitotic apparatus protein 1) This gene encodes a large protein that forms a structural component of the nuclear matrix. The encoded protein interacts with microtubules and plays a role in the formation and organization of the mitotic spindle during cell division. Chromosomal translocation of this gene with the RARA (retinoic acid receptor, alpha) gene on chromosome 17 have been detected in patients with acute promyelocytic leukemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]
IL18BP (HGNC:5987): (interleukin 18 binding protein) The protein encoded by this gene functions as an inhibitor of the proinflammatory cytokine, IL18. It binds IL18, prevents the binding of IL18 to its receptor, and thus inhibits IL18-induced IFN-gamma production, resulting in reduced T-helper type 1 immune responses. This protein is constitutively expressed and secreted in mononuclear cells. Elevated level of this protein is detected in the intestinal tissues of patients with Crohn's disease. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]

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=-0.67).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0573 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NUMA1NM_006185.4 linkuse as main transcriptc.*540C>T 3_prime_UTR_variant 27/27 ENST00000393695.8 NP_006176.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NUMA1ENST00000393695.8 linkuse as main transcriptc.*540C>T 3_prime_UTR_variant 27/271 NM_006185.4 ENSP00000377298 P2Q14980-1

Frequencies

GnomAD3 genomes
AF:
0.0177
AC:
2693
AN:
152204
Hom.:
77
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0592
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00876
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000828
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00106
Gnomad OTH
AF:
0.00957
GnomAD4 exome
AF:
0.00499
AC:
412
AN:
82632
Hom.:
7
Cov.:
0
AF XY:
0.00479
AC XY:
183
AN XY:
38244
show subpopulations
Gnomad4 AFR exome
AF:
0.0652
Gnomad4 AMR exome
AF:
0.00991
Gnomad4 ASJ exome
AF:
0.00235
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00129
Gnomad4 OTH exome
AF:
0.00748
GnomAD4 genome
AF:
0.0178
AC:
2705
AN:
152322
Hom.:
79
Cov.:
33
AF XY:
0.0165
AC XY:
1231
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.0593
Gnomad4 AMR
AF:
0.00875
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00106
Gnomad4 OTH
AF:
0.00947
Alfa
AF:
0.00527
Hom.:
18
Bravo
AF:
0.0203
Asia WGS
AF:
0.00693
AC:
24
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
8.1
DANN
Benign
0.80
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3

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: rs5743679; hg19: chr11-71714033; API