19-41011783-T-C

Variant summary

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

The NM_000767.5(CYP2B6):c.965-515T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,742 control chromosomes in the GnomAD database, including 35,273 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 0.68 (35273 hom., cov: 29)
• Consequence: CYP2B6 NM_000767.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

Genes affected

CYP2B6 (HGNC:2615): (cytochrome P450 family 2 subfamily B member 6) This gene, CYP2B6, encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and its expression is induced by phenobarbital. The enzyme is known to metabolize some xenobiotics, such as the anti-cancer drugs cyclophosphamide and ifosphamide. Transcript variants for this gene have been described; however, it has not been resolved whether these transcripts are in fact produced by this gene or by a closely related pseudogene, CYP2B7. Both the gene and the pseudogene are located in the middle of a CYP2A pseudogene found in a large cluster of cytochrome P450 genes from the CYP2A, CYP2B and CYP2F subfamilies on chromosome 19q. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2B6	NM_000767.5	c.965-515T>C		intron_variant		ENST00000324071.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2B6	ENST00000324071.10	c.965-515T>C		intron_variant		1	NM_000767.5	P1
CYP2B6	ENST00000597612.1	n.460-515T>C		intron_variant, non_coding_transcript_variant		1
CYP2B6	ENST00000593831.1	c.257-515T>C		intron_variant		2
CYP2B6	ENST00000598834.2	c.*406-515T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102651 AN: 151624 Hom.: 35248 Cov.: 29

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.677 AC: 102726 AN: 151742 Hom.: 35273 Cov.: 29 AF XY: 0.682 AC XY: 50577 AN XY: 74126

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.697

Alfa AF: 0.633 Hom.: 51366

Bravo AF: 0.690

Asia WGS AF: 0.728 AC: 2531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.089
Dann	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs6508965; hg19: chr19-41517688;