chr1-171648188-TA-T

Position:

• chr1-171648188-TA-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000261.2(MYOC):​c.604+3819delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.75 (40302 hom., cov: 0)
• Consequence: MYOC NM_000261.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

MYOC (HGNC:7610): (myocilin) MYOC encodes the protein myocilin, which is believed to have a role in cytoskeletal function. MYOC is expressed in many occular tissues, including the trabecular meshwork, and was revealed to be the trabecular meshwork glucocorticoid-inducible response protein (TIGR). The trabecular meshwork is a specialized eye tissue essential in regulating intraocular pressure, and mutations in MYOC have been identified as the cause of hereditary juvenile-onset open-angle glaucoma. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYOC	NM_000261.2	c.604+3819delT		intron_variant		ENST00000037502.11	NP_000252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYOC	ENST00000037502.11	c.604+3819delT		intron_variant		1	NM_000261.2	ENSP00000037502.5
MYOC	ENST00000638471.1	n.130+4293delT		intron_variant		5		ENSP00000491206.1

Frequencies

GnomAD3 genomes AF: 0.748 AC: 108201 AN: 144750 Hom.: 40293 Cov.: 0

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.748 AC: 108226 AN: 144784 Hom.: 40302 Cov.: 0 AF XY: 0.749 AC XY: 52376 AN XY: 69924

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.751

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11295938; hg19: chr1-171617328;