17-68600282-TC-GTTCCAGCGGG

Position:

• chr17-68600282-TC-GTTCCAGCGGG

Variant summary

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

The NM_017565.4(FAM20A):​c.384_385delGAinsCCCGCTGGAAC​(p.Arg128_Lys129delinsSerProLeuGluGln) variant causes a missense, disruptive inframe insertion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM20A NM_017565.4 missense, disruptive_inframe_insertion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.80

Genes affected

FAM20A (HGNC:23015): (FAM20A golgi associated secretory pathway pseudokinase) This locus encodes a protein that is likely secreted and may function in hematopoiesis. A mutation at this locus has been associated with amelogenesis imperfecta and gingival hyperplasia syndrome. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]

LINC01482 (HGNC:51128): (long intergenic non-protein coding RNA 1482)

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_017565.4.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM20A	NM_017565.4	c.384_385delGAinsCCCGCTGGAAC	p.Arg128_Lys129delinsSerProLeuGluGln	missense_variant, disruptive_inframe_insertion		ENST00000592554.2	NP_060035.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM20A	ENST00000592554.2	c.384_385delGAinsCCCGCTGGAAC	p.Arg128_Lys129delinsSerProLeuGluGln	missense_variant, disruptive_inframe_insertion		1	NM_017565.4	ENSP00000468308.1
FAM20A	ENST00000590074.5	n.312_313delGAinsCCCGCTGGAAC		non_coding_transcript_exon_variant	1/12	2		ENSP00000464910.1
LINC01482	ENST00000587999.1	n.198+2136_198+2137delTCinsGTTCCAGCGGG		intron_variant		3
LINC01482	ENST00000589610.5	n.40+8404_40+8405delTCinsGTTCCAGCGGG		intron_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Amelogenesis imperfecta type 1G Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Feb 14, 2024

- -

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: chr17-66596423;