rs1458868

chr2-71149071-C-T

Variant summary

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

The NM_005791.3(MPHOSPH10):c.1666-152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 663,194 control chromosomes in the GnomAD database, including 83,211 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 0.44 (16002 hom., cov: 33)
  • Exomes 𝑓: 0.51 (67209 hom.)
• Consequence: MPHOSPH10 NM_005791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPHOSPH10	NM_005791.3	c.1666-152C>T		intron_variant		ENST00000244230.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH10	ENST00000244230.7	c.1666-152C>T		intron_variant		1	NM_005791.3	P1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67293 AN: 151964 Hom.: 15999 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.473

GnomAD4 exome AF: 0.506 AC: 258661 AN: 511112 Hom.: 67209 Cov.: 6 AF XY: 0.508 AC XY: 136211 AN XY: 268340

Gnomad4 AFR exome AF: 0.263

Gnomad4 AMR exome AF: 0.440

Gnomad4 ASJ exome AF: 0.591

Gnomad4 EAS exome AF: 0.295

Gnomad4 SAS exome AF: 0.508

Gnomad4 FIN exome AF: 0.505

Gnomad4 NFE exome AF: 0.538

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.443 AC: 67315 AN: 152082 Hom.: 16002 Cov.: 33 AF XY: 0.441 AC XY: 32783 AN XY: 74336

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.476

Alfa AF: 0.520 Hom.: 43687

Bravo AF: 0.428

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.8
Dann	Benign	0.53

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: rs1458868; hg19: chr2-71376201;