rs379042

Positions:

• chr20-64164202-G-A
• chr20-64164202-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYT1	ENST00000360149.9	c.-99+12292G>A		intron_variant		1		ENSP00000353269
MYT1	ENST00000644172.2	c.23-25861G>A		intron_variant				ENSP00000493561
MYT1	ENST00000659024.1	c.-99+12292G>A		intron_variant				ENSP00000499493

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

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.284

Alfa AF: 0.276 Hom.: 9946

Bravo AF: 0.271

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs379042; hg19: chr20-62795555;