rs6461049

chr7-1977810-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001013836.2(MAD1L1):c.1505+2643G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,156 control chromosomes in the GnomAD database, including 24,145 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 0.56 (24145 hom., cov: 35)
• Consequence: MAD1L1 NM_001013836.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAD1L1	NM_001013836.2	c.1505+2643G>A		intron_variant		ENST00000265854.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAD1L1	ENST00000265854.12	c.1505+2643G>A		intron_variant		1	NM_001013836.2	P1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 85033 AN: 152038 Hom.: 24126 Cov.: 35

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.553

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.559 AC: 85085 AN: 152156 Hom.: 24145 Cov.: 35 AF XY: 0.560 AC XY: 41640 AN XY: 74386

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.556

Alfa AF: 0.561 Hom.: 40687

Bravo AF: 0.540

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.040
Dann	Benign	0.57

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

Other links and lift over

dbSNP: rs6461049; hg19: chr7-2017445; COSMIC: COSV56229981; COSMIC: COSV56229981;