16-15750191-G-C

Variant names:

• chr16-15750191-G-C
• NM_002474.3:c.2005C>G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_002474.3(MYH11):​c.2005C>G​(p.Arg669Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R669C) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYH11 NM_002474.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00

Genes affected

MYH11 (HGNC:7569): (myosin heavy chain 11) The protein encoded by this gene is a smooth muscle myosin belonging to the myosin heavy chain family. The gene product is a subunit of a hexameric protein that consists of two heavy chain subunits and two pairs of non-identical light chain subunits. It functions as a major contractile protein, converting chemical energy into mechanical energy through the hydrolysis of ATP. A chromosomal rearrangement involving this gene is associated with acute myeloid leukemia of the M4Eo subtype. Mutations in this gene are associated with visceral myopathy, megacystis-microcolon-intestinal hypoperistalsis syndrome 2, and familial thoracic aortic aneurysm 4. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.868

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH11	NM_002474.3	c.2005C>G	p.Arg669Gly	missense_variant	Exon 16 of 41	ENST00000300036.6	NP_002465.1
MYH11	NM_001040113.2	c.2026C>G	p.Arg676Gly	missense_variant	Exon 17 of 43	ENST00000452625.7	NP_001035202.1
MYH11	NM_001040114.2	c.2026C>G	p.Arg676Gly	missense_variant	Exon 17 of 42		NP_001035203.1
MYH11	NM_022844.3	c.2005C>G	p.Arg669Gly	missense_variant	Exon 16 of 42		NP_074035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH11	ENST00000300036.6	c.2005C>G	p.Arg669Gly	missense_variant	Exon 16 of 41	1	NM_002474.3	ENSP00000300036.5
MYH11	ENST00000452625.7	c.2026C>G	p.Arg676Gly	missense_variant	Exon 17 of 43	1	NM_001040113.2	ENSP00000407821.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.20
CADD	Pathogenic	31
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.81	.;.;.;D
Eigen	Uncertain	0.53
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.89	D;D;D;D
M_CAP	Uncertain	0.24	D
MetaRNN	Pathogenic	0.87	D;D;D;D
MetaSVM	Uncertain	0.67	D
MutationAssessor	Benign	1.6	.;.;L;L
PrimateAI	Uncertain	0.53	T
PROVEAN	Pathogenic	-5.0	D;D;.;D
REVEL	Pathogenic	0.83
Sift	Uncertain	0.0020	D;D;.;D
Sift4G	Uncertain	0.0040	D;D;D;D
Polyphen		0.57	.;.;.;P
Vest4		0.75
MutPred		0.63		.;.;Loss of MoRF binding (P = 0.0405);Loss of MoRF binding (P = 0.0405);
MVP		0.95
MPC		1.1
ClinPred		0.99	D
GERP RS		4.4
Varity_R		0.71
gMVP		0.68

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: chr16-15844048;