22-42644801-C-T

Variant names:

• chr22-42644801-C-T
• rs8190404
• NM_000398.7:c.21+4494G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000398.7(CYB5R3):​c.21+4494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,188 control chromosomes in the GnomAD database, including 1,731 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (1731 hom., cov: 33)
• Consequence: CYB5R3 NM_000398.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.191
• Publications: 4 publications found

Genes affected

CYB5R3 (HGNC:2873): (cytochrome b5 reductase 3) This gene encodes cytochrome b5 reductase, which includes a membrane-bound form in somatic cells (anchored in the endoplasmic reticulum, mitochondrial and other membranes) and a soluble form in erythrocytes. The membrane-bound form exists mainly on the cytoplasmic side of the endoplasmic reticulum and functions in desaturation and elongation of fatty acids, in cholesterol biosynthesis, and in drug metabolism. The erythrocyte form is located in a soluble fraction of circulating erythrocytes and is involved in methemoglobin reduction. The membrane-bound form has both membrane-binding and catalytic domains, while the soluble form has only the catalytic domain. Alternate splicing results in multiple transcript variants. Mutations in this gene cause methemoglobinemias. [provided by RefSeq, Jan 2010]

CYB5R3 Gene-Disease associations (from GenCC):

• methemoglobinemia

  Inheritance: AR Classification: DEFINITIVE Submitted by: Illumina
• methemoglobinemia due to deficiency of methemoglobin reductase

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• hereditary methemoglobinemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 22-42644801-C-T is Benign according to our data. Variant chr22-42644801-C-T is described in ClinVar as Benign. ClinVar VariationId is 1274008.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000398.7. 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
	CYB5R3	NM_000398.7	MANE Select	c.21+4494G>A		intron	N/A	NP_000389.1
	CYB5R3	NM_001129819.2		c.-49+1840G>A		intron	N/A	NP_001123291.1
	CYB5R3	NM_001171661.1		c.-49+1840G>A		intron	N/A	NP_001165132.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYB5R3	ENST00000352397.10	TSL:1 MANE Select	c.21+4494G>A		intron	N/A	ENSP00000338461.6
	CYB5R3	ENST00000407332.6	TSL:1	c.21+4494G>A		intron	N/A	ENSP00000384457.2
	CYB5R3	ENST00000361740.9	TSL:2	c.21+4494G>A		intron	N/A	ENSP00000354468.5

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22261 AN: 152070 Hom.: 1725 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22296 AN: 152188 Hom.: 1731 Cov.: 33 AF XY: 0.142 AC XY: 10587 AN XY: 74400

African (AFR) AF: 0.170 AC: 7061 AN: 41510

American (AMR) AF: 0.127 AC: 1940 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0378 AC: 182 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1386 AN: 10602

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10390 AN: 68000

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.149 Hom.: 1087

Bravo AF: 0.150

Asia WGS AF: 0.0430 AC: 156 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.66
PhyloP100		-0.19
PromoterAI		0.13	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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: rs8190404; hg19: chr22-43040807;