2-71130504-C-T

Position:

• chr2-71130504-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000498451.3(MPHOSPH10):​c.-162C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 830,438 control chromosomes in the GnomAD database, including 166,660 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.54 (25028 hom., cov: 35)
  • Exomes 𝑓: 0.64 (141632 hom.)
• Consequence: MPHOSPH10 ENST00000498451.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0670

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 2-71130504-C-T is Benign according to our data. Variant chr2-71130504-C-T is described in ClinVar as [Benign]. Clinvar id is 1222521.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH10	ENST00000498451.3	c.-162C>T		5_prime_UTR_variant	1/5	1
MPHOSPH10	ENST00000468427.2	c.-673C>T		5_prime_UTR_variant	1/11	4
MPHOSPH10	ENST00000695484.2	c.-162C>T		5_prime_UTR_variant, NMD_transcript_variant	1/11

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82735 AN: 152096 Hom.: 25032 Cov.: 35

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.567

GnomAD4 exome AF: 0.638 AC: 432894 AN: 678222 Hom.: 141632 Cov.: 9 AF XY: 0.641 AC XY: 221679 AN XY: 345738

Gnomad4 AFR exome AF: 0.254

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.724

Gnomad4 EAS exome AF: 0.363

Gnomad4 SAS exome AF: 0.634

Gnomad4 FIN exome AF: 0.656

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.621

GnomAD4 genome AF: 0.544 AC: 82755 AN: 152216 Hom.: 25028 Cov.: 35 AF XY: 0.547 AC XY: 40731 AN XY: 74428

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.563

Alfa AF: 0.401 Hom.: 1006

Bravo AF: 0.529

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.93

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: rs1813348; hg19: chr2-71357634; COSMIC: COSV54907692; COSMIC: COSV54907692;