2-71130360-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The ENST00000498451.3(MPHOSPH10):c.-306C>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 0.00708 in 892,788 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0062 (10 hom., cov: 34)
  • Exomes 𝑓: 0.0073 (25 hom.)
• Consequence: MPHOSPH10 ENST00000498451.3 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.695

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 2-71130360-C-T is Benign according to our data. Variant chr2-71130360-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1325930.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 10 AR gene

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.-306C>T		5_prime_UTR_variant	1/5	1
MPHOSPH10	ENST00000468427.2	c.-817C>T		5_prime_UTR_variant	1/11	4
MPHOSPH10	ENST00000695484.2	c.-306C>T		5_prime_UTR_variant, NMD_transcript_variant	1/11

Frequencies

GnomAD3 genomes AF: 0.00621 AC: 946 AN: 152218 Hom.: 10 Cov.: 34

Gnomad AFR AF: 0.00111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00386

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00839

Gnomad OTH AF: 0.00335

GnomAD4 exome AF: 0.00725 AC: 5371 AN: 740452 Hom.: 25 Cov.: 10 AF XY: 0.00703 AC XY: 2729 AN XY: 388164

Gnomad4 AFR exome AF: 0.00121

Gnomad4 AMR exome AF: 0.00255

Gnomad4 ASJ exome AF: 0.00306

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00120

Gnomad4 FIN exome AF: 0.0260

Gnomad4 NFE exome AF: 0.00763

Gnomad4 OTH exome AF: 0.00601

GnomAD4 genome AF: 0.00622 AC: 948 AN: 152336 Hom.: 10 Cov.: 34 AF XY: 0.00673 AC XY: 501 AN XY: 74484

Gnomad4 AFR AF: 0.00111

Gnomad4 AMR AF: 0.00385

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.00842

Gnomad4 OTH AF: 0.00332

Alfa AF: 0.00767 Hom.: 1

Bravo AF: 0.00416

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.8
Dann	Benign	0.80

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: rs184689442; hg19: chr2-71357490;