19-18110837-C-T

Variant summary

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

The NM_001393504.1(MAST3):​c.161+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 519,152 control chromosomes in the GnomAD database, including 53,807 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 ( 17669 hom., cov: 32)
Exomes 𝑓: 0.43 ( 36138 hom. )

Consequence

MAST3
NM_001393504.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276
Variant links:
Genes affected
MAST3 (HGNC:19036): (microtubule associated serine/threonine kinase 3) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in cytoskeleton organization; intracellular signal transduction; and peptidyl-serine phosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAST3NM_001393504.1 linkuse as main transcriptc.161+96C>T intron_variant ENST00000687212.1 NP_001380433.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MAST3ENST00000687212.1 linkuse as main transcriptc.161+96C>T intron_variant NM_001393504.1 ENSP00000509890.1 A0A8I5KST9

Frequencies

GnomAD3 genomes
AF:
0.476
AC:
72395
AN:
151934
Hom.:
17636
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.553
Gnomad AMI
AF:
0.276
Gnomad AMR
AF:
0.483
Gnomad ASJ
AF:
0.461
Gnomad EAS
AF:
0.321
Gnomad SAS
AF:
0.271
Gnomad FIN
AF:
0.503
Gnomad MID
AF:
0.449
Gnomad NFE
AF:
0.454
Gnomad OTH
AF:
0.495
GnomAD4 exome
AF:
0.433
AC:
158857
AN:
367098
Hom.:
36138
AF XY:
0.432
AC XY:
74746
AN XY:
173008
show subpopulations
Gnomad4 AFR exome
AF:
0.560
Gnomad4 AMR exome
AF:
0.462
Gnomad4 ASJ exome
AF:
0.470
Gnomad4 EAS exome
AF:
0.307
Gnomad4 SAS exome
AF:
0.255
Gnomad4 FIN exome
AF:
0.484
Gnomad4 NFE exome
AF:
0.435
Gnomad4 OTH exome
AF:
0.423
GnomAD4 genome
AF:
0.477
AC:
72486
AN:
152054
Hom.:
17669
Cov.:
32
AF XY:
0.477
AC XY:
35447
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.554
Gnomad4 AMR
AF:
0.483
Gnomad4 ASJ
AF:
0.461
Gnomad4 EAS
AF:
0.322
Gnomad4 SAS
AF:
0.272
Gnomad4 FIN
AF:
0.503
Gnomad4 NFE
AF:
0.454
Gnomad4 OTH
AF:
0.491
Alfa
AF:
0.458
Hom.:
19818
Bravo
AF:
0.484
Asia WGS
AF:
0.338
AC:
1179
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
3.7
DANN
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs273506; hg19: chr19-18221647; COSMIC: COSV53220120; API