2-71149071-C-T

Variant names:

• chr2-71149071-C-T
• rs1458868
• NM_005791.3:c.1666-152C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005791.3(MPHOSPH10):​c.1666-152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 663,194 control chromosomes in the GnomAD database, including 83,211 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.44 (16002 hom., cov: 33)
  • Exomes 𝑓: 0.51 (67209 hom.)
• Consequence: MPHOSPH10 NM_005791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 9 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPHOSPH10	NM_005791.3	c.1666-152C>T		intron_variant	Intron 9 of 10	ENST00000244230.7	NP_005782.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPHOSPH10	ENST00000244230.7	c.1666-152C>T		intron_variant	Intron 9 of 10	1	NM_005791.3	ENSP00000244230.2

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67293 AN: 151964 Hom.: 15999 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.473

GnomAD4 exome AF: 0.506 AC: 258661 AN: 511112 Hom.: 67209 Cov.: 6 AF XY: 0.508 AC XY: 136211 AN XY: 268340

African (AFR) AF: 0.263 AC: 3492 AN: 13280

American (AMR) AF: 0.440 AC: 8270 AN: 18806

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 8317 AN: 14072

East Asian (EAS) AF: 0.295 AC: 9323 AN: 31602

South Asian (SAS) AF: 0.508 AC: 22875 AN: 45028

European-Finnish (FIN) AF: 0.505 AC: 22151 AN: 43868

Middle Eastern (MID) AF: 0.562 AC: 1178 AN: 2096

European-Non Finnish (NFE) AF: 0.538 AC: 169073 AN: 314416

Other (OTH) AF: 0.500 AC: 13982 AN: 27944

GnomAD4 genome AF: 0.443 AC: 67315 AN: 152082 Hom.: 16002 Cov.: 33 AF XY: 0.441 AC XY: 32783 AN XY: 74336

African (AFR) AF: 0.273 AC: 11320 AN: 41476

American (AMR) AF: 0.438 AC: 6695 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2060 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1373 AN: 5168

South Asian (SAS) AF: 0.488 AC: 2347 AN: 4814

European-Finnish (FIN) AF: 0.511 AC: 5397 AN: 10560

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36515 AN: 67998

Other (OTH) AF: 0.476 AC: 1005 AN: 2110

Alfa AF: 0.504 Hom.: 63262

Bravo AF: 0.428

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.53
PhyloP100		0.17
Mutation Taster		=100/0	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: rs1458868; hg19: chr2-71376201;