6-83909015-CGT-TCA

Variant names:

• chr6-83909015-CGT-TCA
• NM_016230.4:c.337_339delCGTinsTCA
• CYB5R4 p.Arg113Ser

Variant summary

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

The NM_016230.4(CYB5R4):​c.337_339delCGTinsTCA​(p.Arg113Ser) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R113H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CYB5R4 NM_016230.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.36
• Publications: 0 publications found

Genes affected

CYB5R4 (HGNC:20147): (cytochrome b5 reductase 4) NCB5OR is a flavohemoprotein that contains functional domains found in both cytochrome b5 (CYB5A; MIM 613218) and CYB5 reductase (CYB5R3; MIM 613213) (Zhu et al., 1999 [PubMed 10611283]).[supplied by OMIM, Jan 2010]

RIPPLY2-CYB5R4 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016230.4. 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
	CYB5R4	NM_016230.4	MANE Select	c.337_339delCGTinsTCA	p.Arg113Ser	missense	N/A	NP_057314.2	Q7L1T6
	RIPPLY2-CYB5R4	NM_001400774.1		c.235_237delCGTinsTCA	p.Arg79Ser	missense	N/A	NP_001387703.1	B2R7W7
	RIPPLY2-CYB5R4	NR_174603.1		n.496_498delCGTinsTCA		non_coding_transcript_exon	Exon 5 of 18

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYB5R4	ENST00000369681.10	TSL:1 MANE Select	c.337_339delCGTinsTCA	p.Arg113Ser	missense	N/A	ENSP00000358695.3	Q7L1T6
	CYB5R4	ENST00000942770.1		c.337_339delCGTinsTCA	p.Arg113Ser	missense	N/A	ENSP00000612829.1
	CYB5R4	ENST00000942768.1		c.337_339delCGTinsTCA	p.Arg113Ser	missense	N/A	ENSP00000612827.1

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		4.4

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: chr6-84618734;