rs1408942490

Variant names:

• chr16-82148780-T-A
• rs1408942490
• NM_005792.2:c.434A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-82148780-T-A
• chr16-82148780-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_005792.2(MPHOSPH6):​c.434A>T​(p.Asp145Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MPHOSPH6 NM_005792.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09125194).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPHOSPH6	NM_005792.2	c.434A>T	p.Asp145Val	missense_variant	Exon 5 of 5	ENST00000258169.9	NP_005783.2
MPHOSPH6	XM_011522808.4	c.380A>T	p.Asp127Val	missense_variant	Exon 6 of 6		XP_011521110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPHOSPH6	ENST00000258169.9	c.434A>T	p.Asp145Val	missense_variant	Exon 5 of 5	1	NM_005792.2	ENSP00000258169.4
MPHOSPH6	ENST00000563504.5	c.347A>T	p.Asp116Val	missense_variant	Exon 5 of 5	2		ENSP00000456626.1
MPHOSPH6	ENST00000563100.5	n.380A>T		non_coding_transcript_exon_variant	Exon 6 of 7	5		ENSP00000454996.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Uncertain	0.98
DEOGEN2	Benign	0.015	T;.
Eigen	Benign	-0.52
Eigen_PC	Benign	-0.36
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.83	T;T
M_CAP	Benign	0.0085	T
MetaRNN	Benign	0.091	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.34	N;.
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-2.1	N;N
REVEL	Benign	0.023
Sift	Uncertain	0.0060	D;D
Sift4G	Uncertain	0.022	D;D
Polyphen		0.013	B;.
Vest4		0.15
MutPred		0.34		Loss of disorder (P = 0.0048);.;
MVP		0.46
MPC		0.0014
ClinPred		0.51	D
GERP RS		3.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.12
gMVP		0.10

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: rs1408942490; hg19: chr16-82182385;