rs357752

Variant names:

• chr2-71143688-T-A
• rs357752
• NM_005791.3:c.1447-740T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005791.3(MPHOSPH10):​c.1447-740T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,080 control chromosomes in the GnomAD database, including 6,233 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 0.28 (6233 hom., cov: 31)
• Consequence: MPHOSPH10 NM_005791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 4 publications found

Genes affected

MPHOSPH10 (HGNC:7213): (M-phase phosphoprotein 10) This gene encodes a protein that is phosphorylated during mitosis. The protein localizes to the nucleolus during interphase and to the chromosomes during M phase. The protein associates with the U3 small nucleolar ribonucleoprotein 60-80S complexes and may be involved in pre-rRNA processing. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPHOSPH10	NM_005791.3	c.1447-740T>A		intron_variant	Intron 7 of 10	ENST00000244230.7	NP_005782.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPHOSPH10	ENST00000244230.7	c.1447-740T>A		intron_variant	Intron 7 of 10	1	NM_005791.3	ENSP00000244230.2
MPHOSPH10	ENST00000468427.2	c.1027-740T>A		intron_variant	Intron 7 of 10	4		ENSP00000511582.1
MPHOSPH10	ENST00000694907.2	n.*1080-740T>A		intron_variant	Intron 7 of 10			ENSP00000511583.1
MPHOSPH10	ENST00000695484.2	n.1447-750T>A		intron_variant	Intron 7 of 10			ENSP00000511956.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42454 AN: 151962 Hom.: 6233 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.279 AC: 42480 AN: 152080 Hom.: 6233 Cov.: 31 AF XY: 0.280 AC XY: 20844 AN XY: 74358

African (AFR) AF: 0.201 AC: 8331 AN: 41486

American (AMR) AF: 0.382 AC: 5832 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1466 AN: 5162

South Asian (SAS) AF: 0.338 AC: 1632 AN: 4822

European-Finnish (FIN) AF: 0.250 AC: 2643 AN: 10574

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20566 AN: 67976

Other (OTH) AF: 0.284 AC: 600 AN: 2112

Alfa AF: 0.279 Hom.: 761

Bravo AF: 0.286

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.54
PhyloP100		-0.16
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: rs357752; hg19: chr2-71370818;