12-120534953-TCT-CCG

Variant names:

• chr12-120534953-TCT-CCG
• NM_014868.5:c.142_144delTCTinsCCG
• RNF10 p.Ser48Pro

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4

The NM_001414895.1(LOC128071547):​c.257_259delTCTinsCCG​(p.ValTer86AlaGluext*?) variant causes a stop lost, splice region change. 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LOC128071547 NM_001414895.1 stop_lost, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.12
• Publications: 0 publications found

Genes affected

RNF10 (HGNC:10055): (ring finger protein 10) The protein encoded by this gene contains a ring finger motif, which is known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. EST data suggests the existence of multiple alternatively spliced transcript variants, however, their full length nature is not known. [provided by RefSeq, Jul 2008]

LOC128071547 (HGNC:0):

ACMG classification

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

• PM4: Stoplost variant in NM_001414895.1

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001414895.1. 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
	RNF10	NM_014868.5	MANE Select	c.142_144delTCTinsCCG	p.Ser48Pro	missense	N/A	NP_055683.3
	LOC128071547	NM_001414895.1	MANE Select	c.257_259delTCTinsCCG	p.ValTer86AlaGluext*?	stop_lost splice_region	N/A	NP_001401824.1	A0A6Q8PGS0
	RNF10	NM_001330474.2		c.142_144delTCTinsCCG	p.Ser48Pro	missense	N/A	NP_001317403.1	Q8N5U6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF10	ENST00000325954.9	TSL:1 MANE Select	c.142_144delTCTinsCCG	p.Ser48Pro	missense	N/A	ENSP00000322242.4	Q8N5U6-1
	ENSG00000288623	ENST00000675818.1	MANE Select	c.257_259delTCTinsCCG	p.ValTer86AlaGluext*?	stop_lost splice_region	N/A	ENSP00000502390.1	A0A6Q8PGS0
	RNF10	ENST00000413266.6	TSL:5	c.142_144delTCTinsCCG	p.Ser48Pro	missense	N/A	ENSP00000415682.2	Q8N5U6-2

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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.1

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: chr12-120972756;