Variant chr2-1801658-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001303052.2(MYT1L):c.3276+38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0493 in 1,274,804 control chromosomes in the GnomAD database, including 1,911 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 193 hom., cov: 32)

Exomes 𝑓: 0.050 ( 1718 hom. )

Consequence

MYT1L
NM_001303052.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.10

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BP6

Variant 2-1801658-G-A is Benign according to our data. Variant chr2-1801658-G-A is described in ClinVar as [Benign]. Clinvar id is 1249518.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0928 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.3276+38C>T		intron_variant		ENST00000647738.2	NP_001289981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYT1L	ENST00000647738.2 linkuse as main transcript	c.3276+38C>T		intron_variant			NM_001303052.2	ENSP00000497479		Q9UL68-1
	ENST00000638628.1 linkuse as main transcript	n.346+1356G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0420

AC:

6387

AN:

152146

Hom.:

194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00837

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0485

Gnomad ASJ

AF:

0.0622

Gnomad EAS

AF:

0.0803

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0737

Gnomad MID

AF:

0.0446

Gnomad NFE

AF:

0.0477

Gnomad OTH

AF:

0.0354

GnomAD3 exomes

AF:

0.0594

AC:

13946

AN:

234680

Hom.:

498

AF XY:

0.0612

AC XY:

7771

AN XY:

127036

show subpopulations

Gnomad AFR exome

AF:

0.00750

Gnomad AMR exome

AF:

0.0687

Gnomad ASJ exome

AF:

0.0652

Gnomad EAS exome

AF:

0.0785

Gnomad SAS exome

AF:

0.0959

Gnomad FIN exome

AF:

0.0773

Gnomad NFE exome

AF:

0.0487

Gnomad OTH exome

AF:

0.0524

GnomAD4 exome

AF:

0.0503

AC:

56420

AN:

1122538

Hom.:

1718

Cov.:

AF XY:

0.0522

AC XY:

29933

AN XY:

573768

show subpopulations

Gnomad4 AFR exome

AF:

0.00887

Gnomad4 AMR exome

AF:

0.0694

Gnomad4 ASJ exome

AF:

0.0662

Gnomad4 EAS exome

AF:

0.0854

Gnomad4 SAS exome

AF:

0.0925

Gnomad4 FIN exome

AF:

0.0730

Gnomad4 NFE exome

AF:

0.0431

Gnomad4 OTH exome

AF:

0.0475

GnomAD4 genome

AF:

0.0419

AC:

6385

AN:

152266

Hom.:

193

Cov.:

AF XY:

0.0447

AC XY:

3325

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00837

Gnomad4 AMR

AF:

0.0486

Gnomad4 ASJ

AF:

0.0622

Gnomad4 EAS

AF:

0.0803

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0737

Gnomad4 NFE

AF:

0.0476

Gnomad4 OTH

AF:

0.0346

Alfa

AF:

0.0469

Hom.:

192

Bravo

AF:

0.0390

Asia WGS

AF:

0.0760

AC:

262

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	Aug 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.0030

DANN

Benign

0.59

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