1-100266406-AGC-GGT

Variant names:

• chr1-100266406-AGC-GGT
• NM_003729.4:c.31_33delAGCinsGGT
• RTCA p.Ser11Gly

Variant summary

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

The NM_003729.4(RTCA):​c.31_33delAGCinsGGT​(p.Ser11Gly) variant causes a missense change involving the alteration of a 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 MNV, 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: RTCA NM_003729.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.22
• Publications: 0 publications found

Genes affected

RTCA (HGNC:17981): (RNA 3'-terminal phosphate cyclase) This gene encodes a member of the RNA 3'-phosphate cyclase family. The encoded protein plays a role in RNA metabolism by catalyzing the ATP-dependent conversion of the 3'-phosphate of RNA substrates to a 2',3'-cyclic phosphodiester. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

RTCA-AS1 (HGNC:50573): (RTCA antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003729.4. 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
	RTCA	NM_003729.4	MANE Select	c.31_33delAGCinsGGT	p.Ser11Gly	missense	N/A	NP_003720.1	O00442-1
	RTCA	NM_001130841.2		c.31_33delAGCinsGGT	p.Ser11Gly	missense	N/A	NP_001124313.1	O00442-2
	RTCA-AS1	NR_110434.1		n.-234_-232delGCTinsACC		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RTCA	ENST00000370128.9	TSL:1 MANE Select	c.31_33delAGCinsGGT	p.Ser11Gly	missense	N/A	ENSP00000359146.4	O00442-1
	RTCA	ENST00000260563.4	TSL:1	c.31_33delAGCinsGGT	p.Ser11Gly	missense	N/A	ENSP00000260563.4	O00442-2
	RTCA	ENST00000370126.1	TSL:1	c.31_33delAGCinsGGT	p.Ser11Gly	missense	N/A	ENSP00000359144.1	A6NIC1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-100731962;