Variant chr7-1872586-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001013836.2(MAD1L1):c.1998+25614T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,964 control chromosomes in the GnomAD database, including 10,636 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 0.37 ( 10631 hom., cov: 33)

Exomes 𝑓: 0.45 ( 5 hom. )

Consequence

MAD1L1
NM_001013836.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.47

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]

MAD1L1 links:

ENSG00000286192 (HGNC:):

ENSG00000286192 links:

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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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAD1L1	NM_001013836.2 link	c.1998+25614T>C		intron_variant		ENST00000265854.12	NP_001013858.1	Q9Y6D9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAD1L1	ENST00000265854.12 link	c.1998+25614T>C		intron_variant		1	NM_001013836.2	ENSP00000265854.7		Q9Y6D9-1
ENSG00000286192	ENST00000651235.1 link	n.*4758+25614T>C		intron_variant				ENSP00000498895.1		A0A3B3ITW8

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56353

AN:

151808

Hom.:

10619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.321

Gnomad AMI

AF:

0.439

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.361

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.385

GnomAD4 exome

AF:

0.447

AC:

AN:

Hom.:

AF XY:

0.471

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.667

Gnomad4 NFE exome

AF:

0.417

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.371

AC:

56396

AN:

151926

Hom.:

10631

Cov.:

AF XY:

0.370

AC XY:

27456

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.321

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.361

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.315

Gnomad4 NFE

AF:

0.389

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.393

Hom.:

15639

Bravo

AF:

0.380

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

-1.0

CADD

Benign

0.40

DANN

Benign

0.086

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over