rs667907

chr19-50282129-A-G

Variant summary

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

The NM_001145809.2(MYH14):c.4539+287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,026 control chromosomes in the GnomAD database, including 11,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.36 (11113 hom., cov: 33)
• Consequence: MYH14 NM_001145809.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.633

Genes affected

MYH14 (HGNC:23212): (myosin heavy chain 14) 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-14 (MYO14). Myosins are actin-dependent motor proteins with diverse functions including regulation of cytokinesis, cell motility, and cell polarity. Mutations in this gene result in one form of autosomal dominant hearing impairment. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 19-50282129-A-G is Benign according to our data. Variant chr19-50282129-A-G is described in ClinVar as [Benign]. Clinvar id is 1272242.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH14	NM_001145809.2	c.4539+287A>G		intron_variant		ENST00000642316.2
MYH14	NM_001077186.2	c.4440+287A>G		intron_variant
MYH14	NM_024729.4	c.4416+287A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH14	ENST00000642316.2	c.4539+287A>G		intron_variant			NM_001145809.2

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55311 AN: 151908 Hom.: 11100 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.364 AC: 55354 AN: 152026 Hom.: 11113 Cov.: 33 AF XY: 0.359 AC XY: 26690 AN XY: 74296

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.356

Alfa AF: 0.314 Hom.: 17308

Bravo AF: 0.372

Asia WGS AF: 0.260 AC: 907 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

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.50
Dann	Benign	0.30

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: rs667907; hg19: chr19-50785386;