chr1-171648188-TA-T

Variant names:

• chr1-171648188-TA-T
• rs11295938
• NM_000261.2:c.604+3819delT

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

MYOC Gene-Disease associations (from GenCC):

• glaucoma 1, open angle, A

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• juvenile open angle glaucoma

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
• open-angle glaucoma

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• congenital glaucoma

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYOC	NM_000261.2	c.604+3819delT		intron_variant	Intron 1 of 2	ENST00000037502.11	NP_000252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOC	ENST00000037502.11	c.604+3819delT		intron_variant	Intron 1 of 2	1	NM_000261.2	ENSP00000037502.5
MYOC	ENST00000638471.1	n.130+4293delT		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.824 AC: 32408 AN: 39330

American (AMR) AF: 0.703 AC: 10196 AN: 14512

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2647 AN: 3414

East Asian (EAS) AF: 0.851 AC: 4198 AN: 4932

South Asian (SAS) AF: 0.800 AC: 3592 AN: 4490

European-Finnish (FIN) AF: 0.696 AC: 6157 AN: 8848

Middle Eastern (MID) AF: 0.825 AC: 231 AN: 280

European-Non Finnish (NFE) AF: 0.706 AC: 46683 AN: 66098

Other (OTH) AF: 0.751 AC: 1489 AN: 1984

Alfa AF: 0.561 Hom.: 1013

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11295938; hg19: chr1-171617328;