1-53230379-C-T

Variant summary

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

The NM_002370.4(MAGOH):c.259-1425G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,916 control chromosomes in the GnomAD database, including 6,167 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 0.26 (6167 hom., cov: 31)
• Consequence: MAGOH NM_002370.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

MAGOH (HGNC:6815): (mago homolog, exon junction complex subunit) Drosophila that have mutations in their mago nashi (grandchildless) gene produce progeny with defects in germplasm assembly and germline development. This gene encodes the mammalian mago nashi homolog. In mammals, mRNA expression is not limited to the germ plasm, but is expressed ubiquitously in adult tissues and can be induced by serum stimulation of quiescent fibroblasts. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGOH	NM_002370.4	c.259-1425G>A		intron_variant		ENST00000371470.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGOH	ENST00000371470.8	c.259-1425G>A		intron_variant		1	NM_002370.4	P1
MAGOH	ENST00000495868.1	n.399-1425G>A		intron_variant, non_coding_transcript_variant		1
MAGOH	ENST00000371466.4	c.148-1425G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39688 AN: 151798 Hom.: 6161 Cov.: 31

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.261 AC: 39699 AN: 151916 Hom.: 6167 Cov.: 31 AF XY: 0.264 AC XY: 19587 AN XY: 74222

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.233

Alfa AF: 0.305 Hom.: 12852

Bravo AF: 0.245

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.3
Dann	Benign	0.77

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: rs10788949; hg19: chr1-53696051;