chr20-64155575-G-T

Variant names:

• chr20-64155575-G-T
• rs3003172
• ENST00000360149.9:c.-99+3665G>T

Variant summary

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

The ENST00000360149.9(MYT1):​c.-99+3665G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,072 control chromosomes in the GnomAD database, including 27,843 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 0.60 (27843 hom., cov: 33)
• Consequence: MYT1 ENST00000360149.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYT1	ENST00000360149.9	TSL:1	c.-99+3665G>T		intron	N/A	ENSP00000353269.4
	MYT1	ENST00000928401.1		c.-355-767G>T		intron	N/A	ENSP00000598460.1
	MYT1	ENST00000659024.1		c.-99+3665G>T		intron	N/A	ENSP00000499493.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91604 AN: 151954 Hom.: 27838 Cov.: 33

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.603 AC: 91647 AN: 152072 Hom.: 27843 Cov.: 33 AF XY: 0.599 AC XY: 44549 AN XY: 74340

African (AFR) AF: 0.668 AC: 27734 AN: 41496

American (AMR) AF: 0.559 AC: 8537 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2906 AN: 5174

South Asian (SAS) AF: 0.433 AC: 2085 AN: 4812

European-Finnish (FIN) AF: 0.607 AC: 6424 AN: 10580

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39950 AN: 67940

Other (OTH) AF: 0.579 AC: 1224 AN: 2114

Alfa AF: 0.583 Hom.: 34567

Bravo AF: 0.601

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-0.021
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: rs3003172; hg19: chr20-62786928;