20-64155575-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYT1	ENST00000360149.9	c.-99+3665G>T		intron_variant		1
MYT1	ENST00000644172.2	c.23-34488G>T		intron_variant
MYT1	ENST00000659024.1	c.-99+3665G>T		intron_variant

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

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.579

Alfa AF: 0.579 Hom.: 20742

Bravo AF: 0.601

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3003172; hg19: chr20-62786928;