Variant rs3748989 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001303052.2(MYT1L):c.291G>A(p.Glu97Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,551,574 control chromosomes in the GnomAD database, including 9,420 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1122 hom., cov: 32)

Exomes 𝑓: 0.10 ( 8298 hom. )

Consequence

MYT1L
NM_001303052.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.592

Variant links:

Genes affected

MYT1L (HGNC:7623): (myelin transcription factor 1 like) This gene encodes a member of the zinc finger superfamily of transcription factors whose expression, thus far, has been found only in neuronal tissues. The encoded protein belongs to a novel class of cystein-cystein-histidine-cystein zinc finger proteins that function in the developing mammalian central nervous system. Forced expression of this gene in combination with the basic helix-loop-helix transcription factor NeuroD1 and the transcription factors POU class 3 homeobox 2 and achaete-scute family basic helix-loop-helix transcription factor 1 can convert fetal and postnatal human fibroblasts into induced neuronal cells, which are able to generate action potentials. Mutations in this gene have been associated with an autosomal dominant form of cognitive disability and with autism spectrum disorder. Alternative splicing results in multiple variants. [provided by RefSeq, Jul 2017]

MYT1L links:

MYT1L (HGNC:):

MYT1L links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 2-1943196-C-T is Benign according to our data. Variant chr2-1943196-C-T is described in ClinVar as [Benign]. Clinvar id is 1266661.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-1943196-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.592 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYT1L	NM_001303052.2 linkuse as main transcript	c.291G>A	p.Glu97Glu	synonymous_variant	9/25	ENST00000647738.2	NP_001289981.1	Q9UL68-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYT1L	ENST00000647738.2 linkuse as main transcript	c.291G>A	p.Glu97Glu	synonymous_variant	9/25		NM_001303052.2	ENSP00000497479.2		Q9UL68-1

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17208

AN:

151834

Hom.:

1122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.0701

Gnomad EAS

AF:

0.320

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.0637

Gnomad NFE

AF:

0.0900

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.119

AC:

18339

AN:

154706

Hom.:

1474

AF XY:

0.116

AC XY:

9476

AN XY:

81782

show subpopulations

Gnomad AFR exome

AF:

0.138

Gnomad AMR exome

AF:

0.117

Gnomad ASJ exome

AF:

0.0678

Gnomad EAS exome

AF:

0.331

Gnomad SAS exome

AF:

0.107

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.0907

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.101

AC:

141877

AN:

1399620

Hom.:

8298

Cov.:

AF XY:

0.100

AC XY:

69378

AN XY:

690346

show subpopulations

Gnomad4 AFR exome

AF:

0.137

Gnomad4 AMR exome

AF:

0.113

Gnomad4 ASJ exome

AF:

0.0659

Gnomad4 EAS exome

AF:

0.313

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.0922

Gnomad4 OTH exome

AF:

0.111

GnomAD4 genome

AF:

0.113

AC:

17219

AN:

151954

Hom.:

1122

Cov.:

AF XY:

0.115

AC XY:

8514

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.134

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.0701

Gnomad4 EAS

AF:

0.320

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.111

Gnomad4 NFE

AF:

0.0900

Gnomad4 OTH

AF:

0.0990

Alfa

AF:

0.0946

Hom.:

1481

Bravo

AF:

0.116

Asia WGS

AF:

0.193

AC:

668

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

1.6

DANN

Benign

0.35

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