dbSNP rs2427625: MYT1:c.*458A>C (chr20-64240906-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004535.3(MYT1):c.*458A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 160,026 control chromosomes in the GnomAD database, including 29,697 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.58 ( 28731 hom., cov: 32)

Exomes 𝑓: 0.47 ( 966 hom. )

Consequence

MYT1
NM_004535.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.944

Publications

9 publications found

Variant links:

Genes affected

MYT1 (HGNC:7622): (myelin transcription factor 1) The protein encoded by this gene is a member of a family of neural specific, zinc finger-containing DNA-binding proteins. The protein binds to the promoter regions of proteolipid proteins of the central nervous system and plays a role in the developing nervous system. [provided by RefSeq, Jul 2008]

MYT1 Gene-Disease associations (from GenCC):

craniofacial microsomia
Inheritance: AD Classification: LIMITED Submitted by: G2P

MYT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYT1	NM_004535.3 link	c.*458A>C		3_prime_UTR_variant	Exon 23 of 23	ENST00000328439.6	NP_004526.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
MYT1	ENST00000328439.6 link	c.*458A>C	3_prime_UTR_variant	Exon 23 of 23	1	NM_004535.3	ENSP00000327465.1
MYT1	ENST00000536311.5 link	c.*458A>C	3_prime_UTR_variant	Exon 23 of 23	5		ENSP00000442412.1
MYT1	ENST00000650655.1 link	c.*458A>C	3_prime_UTR_variant	Exon 25 of 25			ENSP00000498616.1

Frequencies

GnomAD3 genomes

AF:

0.584

AC:

88790

AN:

151944

Hom.:

28679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.857

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.450

Gnomad ASJ

AF:

0.644

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.620

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.567

GnomAD4 exome

AF:

0.469

AC:

3739

AN:

7964

Hom.:

966

Cov.:

AF XY:

0.472

AC XY:

1914

AN XY:

4058

show subpopulations

African (AFR)

AF:

0.871

AC:

155

AN:

178

American (AMR)

AF:

0.348

AC:

395

AN:

1134

Ashkenazi Jewish (ASJ)

AF:

0.687

AC:

125

AN:

182

East Asian (EAS)

AF:

0.104

AC:

AN:

240

South Asian (SAS)

AF:

0.629

AC:

297

AN:

472

European-Finnish (FIN)

AF:

0.373

AC:

197

AN:

528

Middle Eastern (MID)

AF:

0.625

AC:

AN:

European-Non Finnish (NFE)

AF:

0.483

AC:

2316

AN:

4792

Other (OTH)

AF:

0.521

AC:

224

AN:

430

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

197

295

394

492

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

144

180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.585

AC:

88894

AN:

152062

Hom.:

28731

Cov.:

AF XY:

0.574

AC XY:

42677

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.857

AC:

35586

AN:

41506

American (AMR)

AF:

0.449

AC:

6865

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.644

AC:

2232

AN:

3468

East Asian (EAS)

AF:

0.139

AC:

716

AN:

5158

South Asian (SAS)

AF:

0.620

AC:

2993

AN:

4826

European-Finnish (FIN)

AF:

0.403

AC:

4252

AN:

10556

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.508

AC:

34505

AN:

67960

Other (OTH)

AF:

0.564

AC:

1186

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1647

3294

4941

6588

8235

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.536

Hom.:

29154

Bravo

AF:

0.595

Asia WGS

AF:

0.420

AC:

1461

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.38

(source)

DANN

Benign

0.43

PhyloP100

-0.94

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over