2-227599009-T-TGGTGGTGGCTGCGGTGGTGGCTGTGGTGGTGGCTGTGGTGGTGGCTGC

Variant names:

• chr2-227599009-T-TGGTGGTGGCTGCGGTGGTGGCTGTGGTGGTGGCTGTGGTGGTGGCTGC
• NM_001395403.1:c.140_141insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

The NM_001395403.1(SCYGR2):​c.140_141insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG​(p.Cys47_Gly48insGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCys) variant causes a disruptive inframe insertion 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 29)
• Consequence: SCYGR2 NM_001395403.1 disruptive_inframe_insertion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.533

Genes affected

SCYGR2 (HGNC:34220): (small cysteine and glycine repeat containing 2) Predicted to be located in intermediate filament. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001395403.1.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCYGR2	NM_001395403.1	c.140_141insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG	p.Cys47_Gly48insGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCys	disruptive_inframe_insertion	Exon 1 of 1	ENST00000641394.1	NP_001382332.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCYGR2	ENST00000641394.1	c.140_141insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG	p.Cys47_Gly48insGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCys	disruptive_inframe_insertion	Exon 1 of 1		NM_001395403.1	ENSP00000493300.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 29

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

May 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SCYGR2: PM2, BP3 -

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: chr2-228463725;