17-8476919-C-G

Variant names:

• chr17-8476919-C-G
• NM_001256012.3:c.5836G>C

Variant summary

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

The NM_001256012.3(MYH10):​c.5836G>C​(p.Glu1946Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYH10 NM_001256012.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.87

Genes affected

MYH10 (HGNC:7568): (myosin heavy chain 10) This gene encodes a member of the myosin superfamily. The protein represents a conventional non-muscle myosin; it should not be confused with the unconventional myosin-10 (MYO10). Myosins are actin-dependent motor proteins with diverse functions including regulation of cytokinesis, cell motility, and cell polarity. Mutations in this gene have been associated with May-Hegglin anomaly and developmental defects in brain and heart. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

NDEL1 (HGNC:17620): (nudE neurodevelopment protein 1 like 1) Enables identical protein binding activity. Involved in chromosome segregation; positive regulation of GTPase activity; and regulation of intracellular protein transport. Located in kinetochore. Biomarker of schizophrenia. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH10	NM_001256012.3	c.5836G>C	p.Glu1946Gln	missense_variant	Exon 42 of 43	ENST00000360416.8	NP_001242941.1
MYH10	NM_001375266.1	c.5773G>C	p.Glu1925Gln	missense_variant	Exon 41 of 42		NP_001362195.1
MYH10	NM_001256095.2	c.5770G>C	p.Glu1924Gln	missense_variant	Exon 41 of 42		NP_001243024.1
MYH10	NM_005964.5	c.5743G>C	p.Glu1915Gln	missense_variant	Exon 40 of 41		NP_005955.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH10	ENST00000360416.8	c.5836G>C	p.Glu1946Gln	missense_variant	Exon 42 of 43	1	NM_001256012.3	ENSP00000353590.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Uncertain:1

May 24, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.5743G>C (p.E1915Q) alteration is located in exon 40 (coding exon 39) of the MYH10 gene. This alteration results from a G to C substitution at nucleotide position 5743, causing the glutamic acid (E) at amino acid position 1915 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.60
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.060
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.42	.;.;T
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D;D;D
M_CAP	Benign	0.066	D
MetaRNN	Uncertain	0.71	D;D;D
MetaSVM	Uncertain	0.18	D
MutationAssessor	Benign	1.7	.;.;L
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-2.0	N;.;N
REVEL	Uncertain	0.58
Sift	Benign	0.060	T;.;T
Sift4G	Benign	0.10	T;T;T
Polyphen		0.18	.;.;B
Vest4		0.67
MutPred		0.43		.;.;Gain of MoRF binding (P = 0.0364);
MVP		0.84
MPC		1.1
ClinPred		0.95	D
GERP RS		5.0
Varity_R		0.34
gMVP		0.37

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-8380237;