20-64212307-C-T

Variant names:

• chr20-64212307-C-T
• rs351881
• NM_004535.3:c.1517+169C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004535.3(MYT1):​c.1517+169C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 149,270 control chromosomes in the GnomAD database, including 479 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 0.062 (479 hom., cov: 31)
• Consequence: MYT1 NM_004535.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYT1	NM_004535.3	c.1517+169C>T		intron_variant	Intron 9 of 22	ENST00000328439.6	NP_004526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYT1	ENST00000328439.6	c.1517+169C>T		intron_variant	Intron 9 of 22	1	NM_004535.3	ENSP00000327465.1

Frequencies

GnomAD3 genomes AF: 0.0622 AC: 9271 AN: 149152 Hom.: 478 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0584

Gnomad AMR AF: 0.0534

Gnomad ASJ AF: 0.0829

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0553

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

GnomAD4 genome AF: 0.0621 AC: 9274 AN: 149270 Hom.: 479 Cov.: 31 AF XY: 0.0603 AC XY: 4394 AN XY: 72886

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0532

Gnomad4 ASJ AF: 0.0829

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.0123

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0547

Alfa AF: 0.0204 Hom.: 13

Bravo AF: 0.0732

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.52

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

LitVar

Other links and lift over

dbSNP: rs351881; hg19: chr20-62843660;