Variant chr17-36497725-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001163735.2(MYO19):c.2757+541G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0644 in 184,406 control chromosomes in the GnomAD database, including 655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.070 ( 628 hom., cov: 32)

Exomes 𝑓: 0.038 ( 27 hom. )

Consequence

MYO19
NM_001163735.2 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.303

Variant links:

Genes affected

MYO19 (HGNC:26234): (myosin XIX) Enables actin binding activity. Involved in regulation of cytokinesis and regulation of mitochondrial fission. Acts upstream of or within mitochondrion migration along actin filament. Located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

MYO19 links:

ZNHIT3 (HGNC:12309): (zinc finger HIT-type containing 3) Predicted to enable thyroid hormone receptor binding activity. Predicted to be involved in box C/D snoRNP assembly; maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); and snoRNA localization. Located in cytoplasm and nucleus. Implicated in PEHO syndrome. [provided by Alliance of Genome Resources, Apr 2022]

ZNHIT3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_addAF=-0.886575).

BP6

Variant 17-36497725-C-T is Benign according to our data. Variant chr17-36497725-C-T is described in ClinVar as [Benign]. Clinvar id is 3056481.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO19	NM_001163735.2 linkuse as main transcript	c.2757+541G>A		intron_variant		ENST00000614623.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO19	ENST00000614623.5 linkuse as main transcript	c.2757+541G>A		intron_variant		2	NM_001163735.2	P1	Q96H55-1

Frequencies

GnomAD3 genomes

AF:

0.0700

AC:

10642

AN:

152064

Hom.:

628

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.0474

Gnomad ASJ

AF:

0.0421

Gnomad EAS

AF:

0.0191

Gnomad SAS

AF:

0.0157

Gnomad FIN

AF:

0.0337

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0357

Gnomad OTH

AF:

0.0736

GnomAD4 exome

AF:

0.0378

AC:

1217

AN:

32224

Hom.:

Cov.:

AF XY:

0.0378

AC XY:

596

AN XY:

15776

show subpopulations

Gnomad4 AFR exome

AF:

0.157

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00971

Gnomad4 EAS exome

AF:

0.0224

Gnomad4 SAS exome

AF:

0.0116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0360

Gnomad4 OTH exome

AF:

0.0362

GnomAD4 genome

AF:

0.0701

AC:

10663

AN:

152182

Hom.:

628

Cov.:

AF XY:

0.0677

AC XY:

5036

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.0474

Gnomad4 ASJ

AF:

0.0421

Gnomad4 EAS

AF:

0.0193

Gnomad4 SAS

AF:

0.0157

Gnomad4 FIN

AF:

0.0337

Gnomad4 NFE

AF:

0.0357

Gnomad4 OTH

AF:

0.0743

Alfa

AF:

0.0544

Hom.:

Bravo

AF:

0.0756

ExAC

AF:

0.00504

AC:

Asia WGS

AF:

0.0330

AC:

113

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ZNHIT3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 18, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.89

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.8

DANN

Benign

0.62

FATHMM_MKL

Benign

0.016

MutationTaster

Benign

1.0

P;P;P;P;P

Vest4

0.033

GERP RS

0.23

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over