ENST00000515795.1:n.408_409insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG

Variant names:

• chr7-246301-G-GGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACA
• ENST00000515795.1:n.408_409insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000515795.1(FAM20C):​n.408_409insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG variant causes a non coding transcript exon 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM20C ENST00000515795.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 0 publications found

Genes affected

FAM20C (HGNC:22140): (FAM20C golgi associated secretory pathway kinase) This gene encodes a member of the family of secreted protein kinases. The encoded protein binds calcium and phosphorylates proteins involved in bone mineralization. Mutations in this gene are associated with the autosomal recessive disorder Raine syndrome. [provided by RefSeq, Apr 2014]

FAM20C Gene-Disease associations (from GenCC):

• lethal osteosclerotic bone dysplasia

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM20C	NM_020223.4	c.864-113_864-112insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG		intron_variant	Intron 3 of 9	ENST00000313766.6	NP_064608.2
FAM20C	XR_001744837.2	n.1414-113_1414-112insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG		intron_variant	Intron 2 of 5
FAM20C	XR_007060116.1	n.1493-113_1493-112insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG		intron_variant	Intron 3 of 6
FAM20C	XR_007060117.1	n.1414-113_1414-112insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM20C	ENST00000515795.1	n.408_409insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG		non_coding_transcript_exon_variant	Exon 1 of 7	1
FAM20C	ENST00000313766.6	c.864-113_864-112insGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGCGACAG		intron_variant	Intron 3 of 9	1	NM_020223.4	ENSP00000322323.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 10

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.3

Splicing

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

Other links and lift over

hg19: chr7-286267;