rs357752

Positions:

• chr2-71143688-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MPHOSPH10	NM_005791.3	c.1447-740T>A		intron_variant		ENST00000244230.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH10	ENST00000244230.7	c.1447-740T>A		intron_variant		1	NM_005791.3	P1
MPHOSPH10	ENST00000468427.2	c.1027-740T>A		intron_variant		4
MPHOSPH10	ENST00000694907.2	c.*1080-740T>A		intron_variant, NMD_transcript_variant
MPHOSPH10	ENST00000695484.2	c.1447-750T>A		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.284

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

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: rs357752; hg19: chr2-71370818;