rs16411

Positions:

• chr11-7665371-G-GTGTT
• chr11-7665371-G-GTGTTTGTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_016229.5(CYB5R2):​c.*2_*3insAACA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,533,698 control chromosomes in the GnomAD database, including 214,762 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.46 (17133 hom., cov: 0)
  • Exomes 𝑓: 0.53 (197629 hom.)
• Consequence: CYB5R2 NM_016229.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

Genes affected

CYB5R2 (HGNC:24376): (cytochrome b5 reductase 2) The protein encoded by this gene belongs to the flavoprotein pyridine nucleotide cytochrome reductase family of proteins. Cytochrome b-type NAD(P)H oxidoreductases are implicated in many processes including cholesterol biosynthesis, fatty acid desaturation and elongation, and respiratory burst in neutrophils and macrophages. Cytochrome b5 reductases have soluble and membrane-bound forms that are the product of alternative splicing. In animal cells, the membrane-bound form binds to the endoplasmic reticulum, where it is a member of a fatty acid desaturation complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

PPFIBP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYB5R2	NM_016229.5	c.*2_*3insAACA		3_prime_UTR_variant	9/9	ENST00000299498.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYB5R2	ENST00000299498.11	c.*2_*3insAACA		3_prime_UTR_variant	9/9	1	NM_016229.5	P1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70316 AN: 151740 Hom.: 17134 Cov.: 0

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.461

GnomAD3 exomes AF: 0.488 AC: 85892 AN: 175990 Hom.: 21318 AF XY: 0.493 AC XY: 46129 AN XY: 93538

Gnomad AFR exome AF: 0.270

Gnomad AMR exome AF: 0.454

Gnomad ASJ exome AF: 0.372

Gnomad EAS exome AF: 0.574

Gnomad SAS exome AF: 0.517

Gnomad FIN exome AF: 0.567

Gnomad NFE exome AF: 0.504

Gnomad OTH exome AF: 0.479

GnomAD4 exome AF: 0.531 AC: 733366 AN: 1381840 Hom.: 197629 Cov.: 40 AF XY: 0.531 AC XY: 361767 AN XY: 681194

Gnomad4 AFR exome AF: 0.283

Gnomad4 AMR exome AF: 0.475

Gnomad4 ASJ exome AF: 0.407

Gnomad4 EAS exome AF: 0.640

Gnomad4 SAS exome AF: 0.542

Gnomad4 FIN exome AF: 0.585

Gnomad4 NFE exome AF: 0.537

Gnomad4 OTH exome AF: 0.505

GnomAD4 genome AF: 0.463 AC: 70331 AN: 151858 Hom.: 17133 Cov.: 0 AF XY: 0.467 AC XY: 34668 AN XY: 74210

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.460

Alfa AF: 0.406 Hom.: 1860

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16411; hg19: chr11-7686602;