rs728546

Variant names:

• chr16-69421625-G-A
• rs728546
• ENST00000686649.1:c.-94+23159G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-69421625-G-A
• chr16-69421625-G-C
• chr16-69421625-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000686649.1(CYB5B):​c.-94+23159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,056 control chromosomes in the GnomAD database, including 38,875 homozygotes. 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: 𝑓 0.71 (38875 hom., cov: 32)
• Consequence: CYB5B ENST00000686649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

CYB5B (HGNC:24374): (cytochrome b5 type B) Enables heme binding activity. Contributes to nitrite reductase (NO-forming) activity. Involved in nitric oxide biosynthetic process. Located in membrane. Part of nitric-oxide synthase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYB5B	ENST00000686649.1	c.-94+23159G>A		intron_variant	Intron 1 of 4			ENSP00000509909.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108074 AN: 151938 Hom.: 38858 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.711 AC: 108135 AN: 152056 Hom.: 38875 Cov.: 32 AF XY: 0.705 AC XY: 52402 AN XY: 74314

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.741

Alfa AF: 0.762 Hom.: 74482

Bravo AF: 0.712

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs728546; hg19: chr16-69455528;