NM_005792.2:c.*232A>G

Variant names:

• chr16-82148499-T-C
• rs1056629
• NM_005792.2:c.*232A>G

Variant summary

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

The NM_005792.2(MPHOSPH6):​c.*232A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 433,450 control chromosomes in the GnomAD database, including 5,805 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 0.14 (2245 hom., cov: 32)
  • Exomes 𝑓: 0.14 (3560 hom.)
• Consequence: MPHOSPH6 NM_005792.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 27 publications found

Genes affected

MPHOSPH6 (HGNC:7214): (M-phase phosphoprotein 6) Predicted to enable RNA binding activity. Involved in maturation of 5.8S rRNA. Located in cytosol; nucleolus; and nucleoplasm. Colocalizes with nuclear exosome (RNase complex). [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005792.2. 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
	MPHOSPH6	NM_005792.2	MANE Select	c.*232A>G		3_prime_UTR	Exon 5 of 5	NP_005783.2	Q99547

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPHOSPH6	ENST00000258169.9	TSL:1 MANE Select	c.*232A>G		3_prime_UTR	Exon 5 of 5	ENSP00000258169.4	Q99547
	MPHOSPH6	ENST00000953188.1		c.*232A>G		3_prime_UTR	Exon 5 of 5	ENSP00000623247.1
	MPHOSPH6	ENST00000880962.1		c.*232A>G		3_prime_UTR	Exon 5 of 5	ENSP00000551021.1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21826 AN: 152034 Hom.: 2230 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.139 AC: 38971 AN: 281298 Hom.: 3560 Cov.: 5 AF XY: 0.139 AC XY: 19920 AN XY: 142956

African (AFR) AF: 0.0585 AC: 519 AN: 8868

American (AMR) AF: 0.383 AC: 3609 AN: 9414

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 1062 AN: 9360

East Asian (EAS) AF: 0.295 AC: 6420 AN: 21746

South Asian (SAS) AF: 0.165 AC: 1436 AN: 8698

European-Finnish (FIN) AF: 0.134 AC: 2369 AN: 17620

Middle Eastern (MID) AF: 0.152 AC: 200 AN: 1314

European-Non Finnish (NFE) AF: 0.112 AC: 20893 AN: 187136

Other (OTH) AF: 0.144 AC: 2463 AN: 17142

GnomAD4 genome AF: 0.144 AC: 21865 AN: 152152 Hom.: 2245 Cov.: 32 AF XY: 0.152 AC XY: 11285 AN XY: 74376

African (AFR) AF: 0.0692 AC: 2872 AN: 41528

American (AMR) AF: 0.340 AC: 5186 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1723 AN: 5180

South Asian (SAS) AF: 0.221 AC: 1062 AN: 4816

European-Finnish (FIN) AF: 0.152 AC: 1613 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8443 AN: 67986

Other (OTH) AF: 0.148 AC: 312 AN: 2114

Alfa AF: 0.130 Hom.: 2020

Bravo AF: 0.155

Asia WGS AF: 0.287 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.28
DANN	Benign	0.56
PhyloP100		-0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1
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: rs1056629; hg19: chr16-82182104;