15-71826660-C-A

Variant names:

• chr15-71826660-C-A
• NM_006901.4:c.7567G>T

Variant summary

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

The NM_006901.4(MYO9A):​c.7567G>T​(p.Gly2523Cys) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYO9A NM_006901.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.42

Genes affected

MYO9A (HGNC:7608): (myosin IXA) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-9 (MYH9). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. They function as actin-based molecular motors. Mutations in this gene have been associated with Bardet-Biedl Syndrome. [provided by RefSeq, Dec 2011]

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=0.25454038).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO9A	NM_006901.4	c.7567G>T	p.Gly2523Cys	missense_variant	Exon 42 of 42	ENST00000356056.10	NP_008832.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO9A	ENST00000356056.10	c.7567G>T	p.Gly2523Cys	missense_variant	Exon 42 of 42	1	NM_006901.4	ENSP00000348349.5
MYO9A	ENST00000561618.5	c.4114G>T	p.Gly1372Cys	missense_variant	Exon 19 of 19	1		ENSP00000457945.1
MYO9A	ENST00000564571	c.*372G>T		3_prime_UTR_variant	Exon 42 of 42	1		ENSP00000456192.1
MYO9A	ENST00000568042.5	c.1309G>T	p.Gly437Cys	missense_variant	Exon 9 of 9	5		ENSP00000457407.1

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

Mar 12, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.7567G>T (p.G2523C) alteration is located in exon 42 (coding exon 41) of the MYO9A gene. This alteration results from a G to T substitution at nucleotide position 7567, causing the glycine (G) at amino acid position 2523 to be replaced by a cysteine (C). 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	Benign	0.14
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.030
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.025	T;T
Eigen	Benign	0.13
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.83	.;T
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.25	T;T
MetaSVM	Benign	-0.29	T
MutationAssessor	Benign	2.0	M;M
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-1.5	N;D
REVEL	Uncertain	0.40
Sift	Uncertain	0.0030	D;D
Sift4G	Uncertain	0.0080	D;D
Polyphen		0.99	D;D
Vest4		0.31
MutPred		0.28		Gain of catalytic residue at M2521 (P = 5e-04);Gain of catalytic residue at M2521 (P = 5e-04);
MVP		0.18
MPC		0.41
ClinPred		0.85	D
GERP RS		3.0
Varity_R		0.16
gMVP		0.29

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: chr15-72119001;