chr20-64164202-G-A

Variant names:

• chr20-64164202-G-A
• rs379042
• ENST00000360149.9:c.-99+12292G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000360149.9(MYT1):​c.-99+12292G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,008 control chromosomes in the GnomAD database, including 5,368 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 0.26 (5368 hom., cov: 32)
• Consequence: MYT1 ENST00000360149.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 5 publications found

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000360149.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYT1	NM_004535.3	MANE Select	c.-636G>A		upstream_gene	N/A	NP_004526.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYT1	ENST00000360149.9	TSL:1	c.-99+12292G>A		intron	N/A	ENSP00000353269.4
	MYT1	ENST00000659024.1		c.-99+12292G>A		intron	N/A	ENSP00000499493.1
	MYT1	ENST00000644172.2		c.23-25861G>A		intron	N/A	ENSP00000493561.2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39914 AN: 151890 Hom.: 5357 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.286

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.263 AC: 39965 AN: 152008 Hom.: 5368 Cov.: 32 AF XY: 0.266 AC XY: 19775 AN XY: 74284

African (AFR) AF: 0.211 AC: 8752 AN: 41458

American (AMR) AF: 0.324 AC: 4943 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2045 AN: 5162

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4808

European-Finnish (FIN) AF: 0.269 AC: 2836 AN: 10562

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18274 AN: 67976

Other (OTH) AF: 0.284 AC: 598 AN: 2106

Alfa AF: 0.273 Hom.: 16574

Bravo AF: 0.271

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.60
PhyloP100		0.62
PromoterAI		0.0014	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs379042; hg19: chr20-62795555;