NM_144607.6:c.506_507delATinsGC

Variant names:

• chr17-7859431-AT-GC
• NM_144607.6:c.506_507delATinsGC
• CYB5D1 p.Tyr169Cys

Variant summary

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

The NM_144607.6(CYB5D1):​c.506_507delATinsGC​(p.Tyr169Cys) 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CYB5D1 NM_144607.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.81
• Publications: 0 publications found

Genes affected

CYB5D1 (HGNC:26516): (cytochrome b5 domain containing 1) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

NAA38 (HGNC:28212): (N-alpha-acetyltransferase 38, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex. Colocalizes with polysome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000280046 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144607.6. 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
	CYB5D1	NM_144607.6	MANE Select	c.506_507delATinsGC	p.Tyr169Cys	missense	N/A	NP_653208.2
	CYB5D1	NM_001330110.2		c.457-19_457-18delATinsGC		intron	N/A	NP_001317039.1	Q6P9G0-2
	NAA38	NM_001330111.2		c.4-2234_4-2233delATinsGC		intron	N/A	NP_001317040.1	I3L4V0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYB5D1	ENST00000332439.5	TSL:1 MANE Select	c.506_507delATinsGC	p.Tyr169Cys	missense	N/A	ENSP00000331479.4	Q6P9G0-1
	CYB5D1	ENST00000570446.1	TSL:4	c.122_123delATinsGC	p.Tyr41Cys	missense	N/A	ENSP00000461852.1	I3NI34
	CYB5D1	ENST00000571846.5	TSL:5	c.457-19_457-18delATinsGC		intron	N/A	ENSP00000459369.1	Q6P9G0-2

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		3.8

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: chr17-7762749;