rs1790099

Variant names:

• chr12-123171986-C-T
• rs1790099
• NM_022782.4:c.2456+4702G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022782.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPHOSPH9	NM_022782.4	MANE Select	c.2456+4702G>A		intron	N/A	NP_073619.3
	MPHOSPH9	NR_103517.2		n.2420+4702G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPHOSPH9	ENST00000606320.6	TSL:5 MANE Select	c.2456+4702G>A		intron	N/A	ENSP00000475489.1
	MPHOSPH9	ENST00000302373.8	TSL:1	n.1934+4702G>A		intron	N/A	ENSP00000304096.5
	MPHOSPH9	ENST00000539024.5	TSL:1	n.1436+4702G>A		intron	N/A	ENSP00000441764.1

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

African (AFR) AF: 0.248 AC: 10273 AN: 41472

American (AMR) AF: 0.681 AC: 10414 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2069 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5165 AN: 5190

South Asian (SAS) AF: 0.673 AC: 3247 AN: 4828

European-Finnish (FIN) AF: 0.730 AC: 7723 AN: 10574

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47833 AN: 68000

Other (OTH) AF: 0.614 AC: 1298 AN: 2114

Alfa AF: 0.668 Hom.: 28713

Bravo AF: 0.565

Asia WGS AF: 0.813 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.77
PhyloP100		-2.8
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: rs1790099; hg19: chr12-123656533;