rs3783819

Variant summary

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

The NM_002431.4(MNAT1):​c.688-30168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,050 control chromosomes in the GnomAD database, including 20,218 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 0.46 ( 20218 hom., cov: 32)

Consequence

MNAT1
NM_002431.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360
Variant links:
Genes affected
MNAT1 (HGNC:7181): (MNAT1 component of CDK activating kinase) The protein encoded by this gene, along with cyclin H and CDK7, forms the CDK-activating kinase (CAK) enzymatic complex. This complex activates several cyclin-associated kinases and can also associate with TFIIH to activate transcription by RNA polymerase II. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MNAT1NM_002431.4 linkuse as main transcriptc.688-30168A>G intron_variant ENST00000261245.9 NP_002422.1 P51948-1A0A024R688

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MNAT1ENST00000261245.9 linkuse as main transcriptc.688-30168A>G intron_variant 1 NM_002431.4 ENSP00000261245.4 P51948-1

Frequencies

GnomAD3 genomes
AF:
0.465
AC:
70605
AN:
151932
Hom.:
20214
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.122
Gnomad AMI
AF:
0.599
Gnomad AMR
AF:
0.610
Gnomad ASJ
AF:
0.588
Gnomad EAS
AF:
0.265
Gnomad SAS
AF:
0.528
Gnomad FIN
AF:
0.674
Gnomad MID
AF:
0.453
Gnomad NFE
AF:
0.611
Gnomad OTH
AF:
0.458
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.464
AC:
70625
AN:
152050
Hom.:
20218
Cov.:
32
AF XY:
0.471
AC XY:
34973
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.122
Gnomad4 AMR
AF:
0.611
Gnomad4 ASJ
AF:
0.588
Gnomad4 EAS
AF:
0.266
Gnomad4 SAS
AF:
0.530
Gnomad4 FIN
AF:
0.674
Gnomad4 NFE
AF:
0.611
Gnomad4 OTH
AF:
0.457
Alfa
AF:
0.583
Hom.:
40082
Bravo
AF:
0.447
Asia WGS
AF:
0.398
AC:
1384
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.6
DANN
Benign
0.52
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs3783819; hg19: chr14-61316264; API