1-58660173-T-TTTTATATTTATATTTATATATTTATATTTATTTTTAATATATATAATATATATTATATATATTAAATATTATATATATTAAATAATATATATATATATATATATAAATAATATATAATAAATATAATATAATATA

Position:

• chr1-58660173-T-TTTTATATTTATATTTATATATTTATATTTATTTTTAATATATATAATATATATTATATATATTAAATATTATATATATTAAATAATATATATATATATATATATAAATAATATATAATAAATATAATATAATATA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001085487.3(MYSM1):​c.2329-19_2329-18insTATATTATATTATATTTATTATATATTATTTATATATATATATATATATATTATTTAATATATATAATATTTAATATATATAATATATATTATATATATTAAAAATAAATATAAATATATAAATATAAATATAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MYSM1 NM_001085487.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00700

Genes affected

MYSM1 (HGNC:29401): (Myb like, SWIRM and MPN domains 1) Enables histone binding activity; peptidase activity; and transcription coactivator activity. Involved in several processes, including chromatin remodeling; monoubiquitinated histone H2A deubiquitination; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of protein-containing complex. Implicated in diabetic retinopathy. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 1-58660173-T-TTTTATATTTATATTTATATATTTATATTTATTTTTAATATATATAATATATATTATATATATTAAATATTATATATATTAAATAATATATATATATATATATATAAATAATATATAATAAATATAATATAATATA is Benign according to our data. Variant chr1-58660173-T-TTTTATATTTATATTTATATATTTATATTTATTTTTAATATATATAATATATATTATATATATTAAATATTATATATATTAAATAATATATATATATATATATATAAATAATATATAATAAATATAATATAATATA is described in ClinVar as [Likely_benign]. Clinvar id is 2120450.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYSM1	NM_001085487.3	c.2329-19_2329-18insTATATTATATTATATTTATTATATATTATTTATATATATATATATATATATTATTTAATATATATAATATTTAATATATATAATATATATTATATATATTAAAAATAAATATAAATATATAAATATAAATATAAA		intron_variant		ENST00000472487.6	NP_001078956.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYSM1	ENST00000472487.6	c.2329-19_2329-18insTATATTATATTATATTTATTATATATTATTTATATATATATATATATATATTATTTAATATATATAATATTTAATATATATAATATATATTATATATATTAAAAATAAATATAAATATATAAATATAAATATAAA		intron_variant		1	NM_001085487.3	ENSP00000418734.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 24

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 30, 2022

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-59125845;