14-20556458-CGA-TGT

Variant names:

• chr14-20556458-CGA-TGT
• NM_001110356.2:c.607_609delTCGinsACA
• RNASE9 p.Ser203Thr

Variant summary

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

The NM_001110356.2(RNASE9):​c.607_609delTCGinsACA​(p.Ser203Thr) variant causes a missense 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 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: RNASE9 NM_001110356.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 0 publications found

Genes affected

RNASE9 (HGNC:20673): (ribonuclease A family member 9 (inactive)) Predicted to enable nucleic acid binding activity. Predicted to act upstream of or within positive regulation of flagellated sperm motility involved in capacitation. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001110356.2. 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
	RNASE9	NM_001110356.2	MANE Select	c.607_609delTCGinsACA	p.Ser203Thr	missense	N/A	NP_001103826.2	A0AAG2RNW0
	RNASE9	NM_001110358.1		c.625_627delTCGinsACA	p.Ser209Thr	missense	N/A	NP_001103828.1	P60153-2
	RNASE9	NM_001110359.1		c.625_627delTCGinsACA	p.Ser209Thr	missense	N/A	NP_001103829.1	P60153-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNASE9	ENST00000554964.6	TSL:1 MANE Select	c.607_609delTCGinsACA	p.Ser203Thr	missense	N/A	ENSP00000450599.2	A0AAG2RNW0
	RNASE9	ENST00000404716.7	TSL:1	c.625_627delTCGinsACA	p.Ser209Thr	missense	N/A	ENSP00000384683.3	P60153-2
	RNASE9	ENST00000553706.5	TSL:1	c.625_627delTCGinsACA	p.Ser209Thr	missense	N/A	ENSP00000450570.1	P60153-2

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		-0.16

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: chr14-21024617;