Variant 1-24065835-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The ENST00000374434.4(MYOM3):c.3534+56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0235 in 1,339,426 control chromosomes in the GnomAD database, including 489 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 46 hom., cov: 33)

Exomes 𝑓: 0.024 ( 443 hom. )

Consequence

MYOM3
ENST00000374434.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.356

Variant links:

Genes affected

MYOM3 (HGNC:26679): (myomesin 3) Predicted to enable actin filament binding activity and protein homodimerization activity. Predicted to be involved in muscle contraction. Predicted to be active in M band. [provided by Alliance of Genome Resources, Apr 2022]

MYOM3 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 1-24065835-C-T is Benign according to our data. Variant chr1-24065835-C-T is described in ClinVar as [Benign]. Clinvar id is 816846.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0176 (2679/152360) while in subpopulation SAS AF= 0.0335 (162/4830). AF 95% confidence interval is 0.0293. There are 46 homozygotes in gnomad4. There are 1296 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 46 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYOM3	NM_152372.4 linkuse as main transcript	c.3534+56G>A		intron_variant		ENST00000374434.4	NP_689585.3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
MYOM3	ENST00000374434.4 linkuse as main transcript	c.3534+56G>A	intron_variant	1	NM_152372.4	ENSP00000363557	P1	Q5VTT5-1
	ENST00000439239.2 linkuse as main transcript	n.404+1562C>T	intron_variant, non_coding_transcript_variant	5
MYOM3	ENST00000338909.9 linkuse as main transcript	c.213+56G>A	intron_variant	2		ENSP00000342689		Q5VTT5-3
MYOM3	ENST00000448831.1 linkuse as main transcript	n.188-9509G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.0176

AC:

2677

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00449

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0170

Gnomad ASJ

AF:

0.0536

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0331

Gnomad FIN

AF:

0.00763

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0245

Gnomad OTH

AF:

0.0177

GnomAD3 exomes

AF:

0.0224

AC:

5572

AN:

248814

Hom.:

AF XY:

0.0245

AC XY:

3305

AN XY:

135142

show subpopulations

Gnomad AFR exome

AF:

0.00415

Gnomad AMR exome

AF:

0.0110

Gnomad ASJ exome

AF:

0.0571

Gnomad EAS exome

AF:

0.000390

Gnomad SAS exome

AF:

0.0368

Gnomad FIN exome

AF:

0.0102

Gnomad NFE exome

AF:

0.0269

Gnomad OTH exome

AF:

0.0284

GnomAD4 exome

AF:

0.0243

AC:

28811

AN:

1187066

Hom.:

443

Cov.:

AF XY:

0.0250

AC XY:

15085

AN XY:

603910

show subpopulations

Gnomad4 AFR exome

AF:

0.00325

Gnomad4 AMR exome

AF:

0.0119

Gnomad4 ASJ exome

AF:

0.0581

Gnomad4 EAS exome

AF:

0.000182

Gnomad4 SAS exome

AF:

0.0372

Gnomad4 FIN exome

AF:

0.0126

Gnomad4 NFE exome

AF:

0.0250

Gnomad4 OTH exome

AF:

0.0258

GnomAD4 genome

AF:

0.0176

AC:

2679

AN:

152360

Hom.:

Cov.:

AF XY:

0.0174

AC XY:

1296

AN XY:

74508

show subpopulations

Gnomad4 AFR

AF:

0.00447

Gnomad4 AMR

AF:

0.0170

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0335

Gnomad4 FIN

AF:

0.00763

Gnomad4 NFE

AF:

0.0245

Gnomad4 OTH

AF:

0.0175

Alfa

AF:

0.0264

Hom.:

Bravo

AF:

0.0176

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0255

EpiControl

AF:

0.0272

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Flexion contracture

Benign:1

Likely benign, no assertion criteria provided

research

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.0

DANN

Benign

0.41

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