NM_016605.3:c.256dupT

Variant names:

• chr5-138344943-C-CT
• NM_016605.3:c.256dupT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_016605.3(FAM53C):​c.256dupT​(p.Ser86PhefsTer14) variant causes a frameshift 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 (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM53C NM_016605.3 frameshift
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 1.71
• Publications: 0 publications found

Genes affected

FAM53C (HGNC:1336): (family with sequence similarity 53 member C) The protein encoded by this gene belongs to the FAM53 protein family. FAM53 protein family members bind to a transcriptional regulator that modulates cell proliferation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016605.3. 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
	FAM53C	NM_016605.3	MANE Select	c.256dupT	p.Ser86PhefsTer14	frameshift	Exon 4 of 5	NP_057689.1	Q9NYF3
	FAM53C	NM_001135647.2		c.256dupT	p.Ser86PhefsTer14	frameshift	Exon 4 of 5	NP_001129119.1	Q9NYF3
	FAM53C	NM_001350195.2		c.226dupT	p.Ser76PhefsTer14	frameshift	Exon 4 of 5	NP_001337124.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM53C	ENST00000239906.10	TSL:1 MANE Select	c.256dupT	p.Ser86PhefsTer14	frameshift	Exon 4 of 5	ENSP00000239906.5	Q9NYF3
	FAM53C	ENST00000434981.6	TSL:1	c.256dupT	p.Ser86PhefsTer14	frameshift	Exon 4 of 5	ENSP00000403705.2	Q9NYF3
	FAM53C	ENST00000513056.5	TSL:1	c.137-452dupT		intron	N/A	ENSP00000425154.1	D6RE00

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Autism (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr5-137680632;