1-53230379-C-T

Variant names:

• chr1-53230379-C-T
• rs10788949
• NM_002370.4:c.259-1425G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002370.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGOH	NM_002370.4	MANE Select	c.259-1425G>A		intron	N/A	NP_002361.1	P61326-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGOH	ENST00000371470.8	TSL:1 MANE Select	c.259-1425G>A		intron	N/A	ENSP00000360525.3	P61326-1
	MAGOH	ENST00000495868.1	TSL:1	n.399-1425G>A		intron	N/A
	MAGOH	ENST00000890248.1		c.376-1425G>A		intron	N/A	ENSP00000560307.1

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

African (AFR) AF: 0.112 AC: 4625 AN: 41458

American (AMR) AF: 0.245 AC: 3732 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2332 AN: 5166

South Asian (SAS) AF: 0.167 AC: 804 AN: 4816

European-Finnish (FIN) AF: 0.407 AC: 4280 AN: 10514

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22138 AN: 67928

Other (OTH) AF: 0.233 AC: 492 AN: 2108

Alfa AF: 0.293 Hom.: 19365

Bravo AF: 0.245

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.77
PhyloP100		-0.042
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10788949; hg19: chr1-53696051;