17-18118293-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_016239.4(MYO15A):c.-219-289G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,940 control chromosomes in the GnomAD database, including 17,996 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (17996 hom., cov: 32)
• Consequence: MYO15A NM_016239.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.327

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 17-18118293-G-A is Benign according to our data. Variant chr17-18118293-G-A is described in ClinVar as [Benign]. Clinvar id is 1261079.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO15A	NM_016239.4	c.-219-289G>A		intron_variant		ENST00000647165.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO15A	ENST00000647165.2	c.-219-289G>A		intron_variant			NM_016239.4	P1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70177 AN: 151822 Hom.: 17948 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.434

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.463 AC: 70279 AN: 151940 Hom.: 17996 Cov.: 32 AF XY: 0.472 AC XY: 35074 AN XY: 74252

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.433

Alfa AF: 0.362 Hom.: 2883

Bravo AF: 0.471

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
Dann	Benign	0.18

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: rs712267; hg19: chr17-18021607; COSMIC: COSV52764444; COSMIC: COSV52764444;