rs6673692

chr1-53231467-A-G

Variant summary

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

The NM_002370.4(MAGOH):c.258+2075T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,106 control chromosomes in the GnomAD database, including 17,581 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 0.47 (17581 hom., cov: 33)
• Consequence: MAGOH NM_002370.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGOH	NM_002370.4	c.258+2075T>C		intron_variant		ENST00000371470.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGOH	ENST00000371470.8	c.258+2075T>C		intron_variant		1	NM_002370.4	P1
MAGOH	ENST00000495868.1	n.398+2075T>C		intron_variant, non_coding_transcript_variant		1
MAGOH	ENST00000371466.4	c.148-2513T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71295 AN: 151988 Hom.: 17567 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.469 AC: 71341 AN: 152106 Hom.: 17581 Cov.: 33 AF XY: 0.464 AC XY: 34480 AN XY: 74348

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.465

Alfa AF: 0.525 Hom.: 20468

Bravo AF: 0.463

Asia WGS AF: 0.387 AC: 1346 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.3
Dann	Benign	0.73

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: rs6673692; hg19: chr1-53697139;