rs16411

Variant names:

• chr11-7665371-G-GTGTT
• rs16411
• NM_016229.5:c.829_*2dupAACA

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_016229.5(CYB5R2):​c.829_*2dupAACA 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:9250): (PPFIA binding protein 2) This gene encodes a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. The encoded protein is a beta liprin and plays a role in axon guidance and neuronal synapse development by recruiting LAR protein-tyrosine phosphatases to the plasma membrane. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYB5R2	NM_016229.5	c.829_*2dupAACA		3_prime_UTR_variant	Exon 9 of 9	ENST00000299498.11	NP_057313.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYB5R2	ENST00000299498	c.829_*2dupAACA		3_prime_UTR_variant	Exon 9 of 9	1	NM_016229.5	ENSP00000299498.6

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

GnomAD2 exomes AF: 0.488 AC: 85892 AN: 175990 AF XY: 0.493

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 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 AC: 8846 AN: 31306

Gnomad4 AMR exome AF: 0.475 AC: 15435 AN: 32470

Gnomad4 ASJ exome AF: 0.407 AC: 9207 AN: 22646

Gnomad4 EAS exome AF: 0.640 AC: 24568 AN: 38410

Gnomad4 SAS exome AF: 0.542 AC: 40861 AN: 75322

Gnomad4 FIN exome AF: 0.585 AC: 29809 AN: 50950

Gnomad4 NFE exome AF: 0.537 AC: 573495 AN: 1068010

Gnomad4 Remaining exome AF: 0.505 AC: 28911 AN: 57248

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 AC: 0.294851 AN: 0.294851

Gnomad4 AMR AF: 0.472 AC: 0.472291 AN: 0.472291

Gnomad4 ASJ AF: 0.416 AC: 0.41609 AN: 0.41609

Gnomad4 EAS AF: 0.612 AC: 0.612277 AN: 0.612277

Gnomad4 SAS AF: 0.537 AC: 0.53736 AN: 0.53736

Gnomad4 FIN AF: 0.574 AC: 0.57432 AN: 0.57432

Gnomad4 NFE AF: 0.532 AC: 0.532484 AN: 0.532484

Gnomad4 OTH AF: 0.460 AC: 0.459562 AN: 0.459562

Alfa AF: 0.406 Hom.: 1860

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=100/0	polymorphism (auto)

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; COSMIC: COSV55085034; COSMIC: COSV55085034;