Menu
GeneBe

2-1801717-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001303052.2(MYT1L):c.3255T>C(p.Asp1085=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 1,610,066 control chromosomes in the GnomAD database, including 2,403 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.044 ( 201 hom., cov: 32)
Exomes 𝑓: 0.051 ( 2202 hom. )

Consequence

MYT1L
NM_001303052.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.216
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-1801717-A-G is Benign according to our data. Variant chr2-1801717-A-G is described in ClinVar as [Benign]. Clinvar id is 1282563.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.216 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYT1LNM_001303052.2 linkuse as main transcriptc.3255T>C p.Asp1085= synonymous_variant 23/25 ENST00000647738.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYT1LENST00000647738.2 linkuse as main transcriptc.3255T>C p.Asp1085= synonymous_variant 23/25 NM_001303052.2 Q9UL68-1
ENST00000638628.1 linkuse as main transcriptn.346+1415A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0441
AC:
6717
AN:
152174
Hom.:
201
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0156
Gnomad AMI
AF:
0.0757
Gnomad AMR
AF:
0.0498
Gnomad ASJ
AF:
0.0622
Gnomad EAS
AF:
0.0796
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0739
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0476
Gnomad OTH
AF:
0.0388
GnomAD3 exomes
AF:
0.0607
AC:
14962
AN:
246492
Hom.:
535
AF XY:
0.0625
AC XY:
8342
AN XY:
133458
show subpopulations
Gnomad AFR exome
AF:
0.0166
Gnomad AMR exome
AF:
0.0699
Gnomad ASJ exome
AF:
0.0656
Gnomad EAS exome
AF:
0.0789
Gnomad SAS exome
AF:
0.0960
Gnomad FIN exome
AF:
0.0774
Gnomad NFE exome
AF:
0.0487
Gnomad OTH exome
AF:
0.0520
GnomAD4 exome
AF:
0.0509
AC:
74212
AN:
1457774
Hom.:
2202
Cov.:
29
AF XY:
0.0525
AC XY:
38078
AN XY:
724970
show subpopulations
Gnomad4 AFR exome
AF:
0.0184
Gnomad4 AMR exome
AF:
0.0705
Gnomad4 ASJ exome
AF:
0.0670
Gnomad4 EAS exome
AF:
0.0856
Gnomad4 SAS exome
AF:
0.0940
Gnomad4 FIN exome
AF:
0.0730
Gnomad4 NFE exome
AF:
0.0450
Gnomad4 OTH exome
AF:
0.0500
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0442
AC:
6730
AN:
152292
Hom.:
201
Cov.:
32
AF XY:
0.0473
AC XY:
3518
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0160
Gnomad4 AMR
AF:
0.0499
Gnomad4 ASJ
AF:
0.0622
Gnomad4 EAS
AF:
0.0796
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.0739
Gnomad4 NFE
AF:
0.0476
Gnomad4 OTH
AF:
0.0379
Alfa
AF:
0.0464
Hom.:
222
Bravo
AF:
0.0418
Asia WGS
AF:
0.0780
AC:
271
AN:
3478
EpiCase
AF:
0.0466
EpiControl
AF:
0.0485

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
2.4
Dann
Benign
0.50

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.

Other links and lift over

dbSNP: rs2288179; hg19: chr2-1805489; COSMIC: COSV67702219; API