17-18150908-G-C

Position:

• chr17-18150908-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016239.4(MYO15A):​c.7468G>C​(p.Ala2490Pro) 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. 16/20 in silico tools predict a benign 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. A2490T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYO15A NM_016239.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

Genes affected

MYO15A (HGNC:7594): (myosin XVA) This gene encodes an unconventional myosin. This protein differs from other myosins in that it has a long N-terminal extension preceding the conserved motor domain. Studies in mice suggest that this protein is necessary for actin organization in the hair cells of the cochlea. Mutations in this gene have been associated with profound, congenital, neurosensory, nonsyndromal deafness. This gene is located within the Smith-Magenis syndrome region on chromosome 17. Read-through transcripts containing an upstream gene and this gene have been identified, but they are not thought to encode a fusion protein. Several alternatively spliced transcript variants have been described, but their full length sequences have not been determined. [provided by RefSeq, Jul 2008]

LOC124903944 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.016117215).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO15A	NM_016239.4	c.7468G>C	p.Ala2490Pro	missense_variant	38/66	ENST00000647165.2	NP_057323.3
MYO15A	XM_017024715.3	c.7471G>C	p.Ala2491Pro	missense_variant	36/64		XP_016880204.1
MYO15A	XM_017024714.3	c.7408G>C	p.Ala2470Pro	missense_variant	35/63		XP_016880203.1
LOC124903944	XR_007065652.1	n.377+695C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO15A	ENST00000647165.2	c.7468G>C	p.Ala2490Pro	missense_variant	38/66		NM_016239.4	ENSP00000495481.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.055
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	3.4
DANN	Benign	0.69
DEOGEN2	Benign	0.0029	T;T;T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.00045	N
LIST_S2	Benign	0.42	T;.;T
M_CAP	Benign	0.038	D
MetaRNN	Benign	0.016	T;T;T
MetaSVM	Benign	-0.80	T
MutationAssessor	Benign	-2.4	.;N;N
PrimateAI	Benign	0.35	T
PROVEAN	Benign	3.0	.;N;.
REVEL	Benign	0.18
Sift	Benign	1.0	.;T;.
Sift4G	Benign	1.0	T;T;.
Polyphen		0.0	.;B;B
Vest4		0.10
MutPred		0.11		Gain of glycosylation at A2490 (P = 0.0039);Gain of glycosylation at A2490 (P = 0.0039);Gain of glycosylation at A2490 (P = 0.0039);
MVP		0.29
ClinPred		0.025	T
GERP RS		-0.71
Varity_R		0.062
gMVP		0.27

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: rs16960959; hg19: chr17-18054222;