Genetic Variant NM_001395403.1:c.140_141insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG (chr2-227599009-T-TGGTGGTGGCTGCGGTGGTGGCTGTGGTGGTGGCTGTGGTGGTGGCTGC) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. 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. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 29)

Consequence

SCYGR2
NM_001395403.1 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.533

Publications

0 publications found

Variant links:

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]

SCYGR2 links:

ENSG00000296787 (HGNC:):

ENSG00000296787 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001395403.1.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395403.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCYGR2	NM_001395403.1	MANE Select	c.140_141insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG	p.Cys47_Gly48insGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCys	disruptive_inframe_insertion	Exon 1 of 1	NP_001382332.1	A0A286YFB4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SCYGR2	ENST00000641394.1	MANE Select	c.140_141insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG	p.Cys47_Gly48insGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCysGlyGlyGlyCys	disruptive_inframe_insertion	Exon 1 of 1	ENSP00000493300.1	A0A286YFB4
ENSG00000296787	ENST00000741985.1		n.189-8879_189-8878insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG		intron	N/A
ENSG00000296787	ENST00000741986.1		n.399-8879_399-8878insTGGTGGTGGCTGTGGTGGTGGCTGCGGTGGTGGCTGCGGTGGTGGCTG		intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.53

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over