chr7-2132820-G-A

Variant summary

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

The NM_001013836.2(MAD1L1):​c.1073+16332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,152 control chromosomes in the GnomAD database, including 7,453 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 0.28 ( 7453 hom., cov: 33)

Consequence

MAD1L1
NM_001013836.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.514
Variant links:
Genes affected
MAD1L1 (HGNC:6762): (mitotic arrest deficient 1 like 1) MAD1L1 is a component of the mitotic spindle-assembly checkpoint that prevents the onset of anaphase until all chromosome are properly aligned at the metaphase plate. MAD1L1 functions as a homodimer and interacts with MAD2L1. MAD1L1 may play a role in cell cycle control and tumor suppression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAD1L1NM_001013836.2 linkuse as main transcriptc.1073+16332C>T intron_variant ENST00000265854.12 NP_001013858.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MAD1L1ENST00000265854.12 linkuse as main transcriptc.1073+16332C>T intron_variant 1 NM_001013836.2 ENSP00000265854 P1Q9Y6D9-1

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42763
AN:
152034
Hom.:
7453
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0724
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.393
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.506
Gnomad SAS
AF:
0.341
Gnomad FIN
AF:
0.312
Gnomad MID
AF:
0.213
Gnomad NFE
AF:
0.358
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42759
AN:
152152
Hom.:
7453
Cov.:
33
AF XY:
0.285
AC XY:
21188
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.0721
Gnomad4 AMR
AF:
0.393
Gnomad4 ASJ
AF:
0.276
Gnomad4 EAS
AF:
0.506
Gnomad4 SAS
AF:
0.341
Gnomad4 FIN
AF:
0.312
Gnomad4 NFE
AF:
0.358
Gnomad4 OTH
AF:
0.318
Alfa
AF:
0.350
Hom.:
15044
Bravo
AF:
0.280
Asia WGS
AF:
0.398
AC:
1384
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.2
DANN
Benign
0.82

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: rs3778991; hg19: chr7-2172455; API