rs1790099

chr12-123171986-C-T

Variant summary

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

The NM_022782.4(MPHOSPH9):c.2456+4702G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,140 control chromosomes in the GnomAD database, including 29,553 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 0.58 (29553 hom., cov: 32)
• Consequence: MPHOSPH9 NM_022782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

Genes affected

MPHOSPH9 (HGNC:7215): (M-phase phosphoprotein 9) Located in Golgi apparatus and centriole. Implicated in multiple sclerosis. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPHOSPH9	NM_022782.4	c.2456+4702G>A		intron_variant		ENST00000606320.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH9	ENST00000606320.6	c.2456+4702G>A		intron_variant		5	NM_022782.4	P1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88837 AN: 152022 Hom.: 29546 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.584 AC: 88864 AN: 152140 Hom.: 29553 Cov.: 32 AF XY: 0.591 AC XY: 43993 AN XY: 74380

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.614

Alfa AF: 0.670 Hom.: 16500

Bravo AF: 0.565

Asia WGS AF: 0.813 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.19
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: rs1790099; hg19: chr12-123656533;