19-50210092-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_001145809.2(MYH14):c.-3-271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.028 (33 hom., cov: 17)
• Consequence: MYH14 NM_001145809.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0340

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=-1.0).
• BP6: Variant 19-50210092-G-A is Benign according to our data. Variant chr19-50210092-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1214402.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0284 (2200/77594) while in subpopulation AMR AF= 0.0343 (149/4348). AF 95% confidence interval is 0.0322. There are 33 homozygotes in gnomad4. There are 1043 alleles in male gnomad4 subpopulation. Median coverage is 17. This position pass quality control queck.
• BS2: High AC in GnomAd at 2202 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH14	NM_001145809.2	c.-3-271G>A		intron_variant		ENST00000642316.2
MYH14	NM_001077186.2	c.-3-271G>A		intron_variant
MYH14	NM_024729.4	c.-3-271G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH14	ENST00000642316.2	c.-3-271G>A		intron_variant			NM_001145809.2

Frequencies

GnomAD3 genomes AF: 0.0284 AC: 2202 AN: 77564 Hom.: 33 Cov.: 17

Gnomad AFR AF: 0.00799

Gnomad AMI AF: 0.0332

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0546

Gnomad EAS AF: 0.000913

Gnomad SAS AF: 0.0270

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0758

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0284 AC: 2200 AN: 77594 Hom.: 33 Cov.: 17 AF XY: 0.0311 AC XY: 1043 AN XY: 33582

Gnomad4 AFR AF: 0.00798

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.0546

Gnomad4 EAS AF: 0.000913

Gnomad4 SAS AF: 0.0264

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0336

Gnomad4 OTH AF: 0.0277

Alfa AF: 0.0226 Hom.: 5

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.1
Dann	Benign	0.36

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: rs189335033; hg19: chr19-50713349;