chr2-71130375-C-T

Position:

• chr2-71130375-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.-291C>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 0.0138 in 851,090 control chromosomes in the GnomAD database, including 589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.041 (374 hom., cov: 34)
  • Exomes 𝑓: 0.0080 (215 hom.)
• Consequence: MPHOSPH10 ENST00000498451.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.621

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=-0.85).
• BP6: Variant 2-71130375-C-T is Benign according to our data. Variant chr2-71130375-C-T is described in ClinVar as [Benign]. Clinvar id is 1237378.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 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.-291C>T		5_prime_UTR_variant	1/5	1
MPHOSPH10	ENST00000468427.2	c.-802C>T		5_prime_UTR_variant	1/11	4
MPHOSPH10	ENST00000695484.2	c.-291C>T		5_prime_UTR_variant, NMD_transcript_variant	1/11

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6192 AN: 152192 Hom.: 372 Cov.: 34

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00961

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00304

Gnomad OTH AF: 0.0282

GnomAD4 exome AF: 0.00800 AC: 5589 AN: 698780 Hom.: 215 Cov.: 9 AF XY: 0.00744 AC XY: 2737 AN XY: 367962

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.00899

Gnomad4 ASJ exome AF: 0.00122

Gnomad4 EAS exome AF: 0.00544

Gnomad4 SAS exome AF: 0.0127

Gnomad4 FIN exome AF: 0.000106

Gnomad4 NFE exome AF: 0.00269

Gnomad4 OTH exome AF: 0.0164

GnomAD4 genome AF: 0.0407 AC: 6193 AN: 152310 Hom.: 374 Cov.: 34 AF XY: 0.0388 AC XY: 2891 AN XY: 74490

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00963

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00304

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0310 Hom.: 47

Bravo AF: 0.0469

Asia WGS AF: 0.0150 AC: 53 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	Nov 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs11126320; hg19: chr2-71357505;