NM_153611.6:c.-111-1558G>T

Variant names:

• chr11-61359386-C-A
• rs4939517
• NM_153611.6:c.-111-1558G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_153611.6(CYB561A3):​c.-111-1558G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: CYB561A3 NM_153611.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 6 publications found

Genes affected

CYB561A3 (HGNC:23014): (cytochrome b561 family member A3) Predicted to enable transmembrane ascorbate ferrireductase activity. Predicted to be involved in cellular iron ion homeostasis. Located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153611.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYB561A3	NM_153611.6	MANE Select	c.-111-1558G>T		intron	N/A	NP_705839.3
	CYB561A3	NM_001300763.2		c.-111-1558G>T		intron	N/A	NP_001287692.1
	CYB561A3	NM_001161454.1		c.-229-1558G>T		intron	N/A	NP_001154926.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYB561A3	ENST00000294072.9	TSL:1 MANE Select	c.-111-1558G>T		intron	N/A	ENSP00000294072.4
	CYB561A3	ENST00000540755.5	TSL:1	n.-111-1558G>T		intron	N/A	ENSP00000445561.1
	CYB561A3	ENST00000537364.5	TSL:2	c.-1669G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 4	ENSP00000438725.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.63
PhyloP100		0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4939517; hg19: chr11-61126858;