chr2-71130580-G-C

Position:

• chr2-71130580-G-C

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.-86G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 1,415,796 control chromosomes in the GnomAD database, including 68,437 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.30 (6911 hom., cov: 34)
  • Exomes 𝑓: 0.31 (61526 hom.)
• Consequence: MPHOSPH10 ENST00000498451.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.637

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=-0.89).
• BP6: Variant 2-71130580-G-C is Benign according to our data. Variant chr2-71130580-G-C is described in ClinVar as [Benign]. Clinvar id is 1250785.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.381 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.-86G>C		5_prime_UTR_variant	1/5	1
MPHOSPH10	ENST00000468427.2	c.-597G>C		5_prime_UTR_variant	1/11	4
MPHOSPH10	ENST00000695484.2	c.-86G>C		5_prime_UTR_variant, NMD_transcript_variant	1/11
MPHOSPH10	ENST00000694907.2			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45220 AN: 152132 Hom.: 6906 Cov.: 34

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.310 AC: 392015 AN: 1263546 Hom.: 61526 Cov.: 19 AF XY: 0.311 AC XY: 192452 AN XY: 618418

Gnomad4 AFR exome AF: 0.267

Gnomad4 AMR exome AF: 0.415

Gnomad4 ASJ exome AF: 0.295

Gnomad4 EAS exome AF: 0.302

Gnomad4 SAS exome AF: 0.334

Gnomad4 FIN exome AF: 0.253

Gnomad4 NFE exome AF: 0.310

Gnomad4 OTH exome AF: 0.303

GnomAD4 genome AF: 0.297 AC: 45257 AN: 152250 Hom.: 6911 Cov.: 34 AF XY: 0.298 AC XY: 22160 AN XY: 74436

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.297

Alfa AF: 0.290 Hom.: 818

Bravo AF: 0.305

Asia WGS AF: 0.290 AC: 1006 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	-0.89
CADD	Benign	6.5
DANN	Benign	0.69

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: rs981947; hg19: chr2-71357710; COSMIC: COSV54906148; COSMIC: COSV54906148;