ENST00000498451.3:c.-86G>C

Variant names:

• chr2-71130580-G-C
• rs981947
• ENST00000498451.3:c.-86G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498451.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPHOSPH10	NM_005791.3	MANE Select	c.-86G>C		upstream_gene	N/A	NP_005782.1	O00566

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPHOSPH10	ENST00000498451.3	TSL:1	c.-86G>C		5_prime_UTR	Exon 1 of 5	ENSP00000475545.1	U3KQ48
	MPHOSPH10	ENST00000468427.2	TSL:4	c.-597G>C		5_prime_UTR	Exon 1 of 11	ENSP00000511582.1	A0A8Q3WK70
	MPHOSPH10	ENST00000695484.2		n.-86G>C		non_coding_transcript_exon	Exon 1 of 11	ENSP00000511956.1	A0A8Q3WKH7

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

African (AFR) AF: 0.267 AC: 7736 AN: 28948

American (AMR) AF: 0.415 AC: 11041 AN: 26616

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 6051 AN: 20524

East Asian (EAS) AF: 0.302 AC: 10701 AN: 35420

South Asian (SAS) AF: 0.334 AC: 23098 AN: 69212

European-Finnish (FIN) AF: 0.253 AC: 10002 AN: 39526

Middle Eastern (MID) AF: 0.268 AC: 1067 AN: 3986

European-Non Finnish (NFE) AF: 0.310 AC: 306332 AN: 986604

Other (OTH) AF: 0.303 AC: 15987 AN: 52710

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

African (AFR) AF: 0.263 AC: 10930 AN: 41550

American (AMR) AF: 0.389 AC: 5954 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.283 AC: 1465 AN: 5172

South Asian (SAS) AF: 0.339 AC: 1639 AN: 4830

European-Finnish (FIN) AF: 0.250 AC: 2656 AN: 10604

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20574 AN: 67998

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.290 Hom.: 818

Bravo AF: 0.305

Asia WGS AF: 0.290 AC: 1006 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.69
PhyloP100		0.64
PromoterAI		-0.063	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

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