19-41016164-G-C

Variant names:

• chr19-41016164-G-C
• rs8109848
• NM_000767.5:c.1295-482G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000767.5(CYP2B6):​c.1295-482G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,910 control chromosomes in the GnomAD database, including 6,088 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 0.26 (6088 hom., cov: 30)
• Consequence: CYP2B6 NM_000767.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.688
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2B6	NM_000767.5	c.1295-482G>C		intron_variant	Intron 8 of 8	ENST00000324071.10	NP_000758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2B6	ENST00000324071.10	c.1295-482G>C		intron_variant	Intron 8 of 8	1	NM_000767.5	ENSP00000324648.2
CYP2B6	ENST00000597612.1	n.648-482G>C		intron_variant	Intron 2 of 2	1
CYP2B6	ENST00000593831.1	c.587-482G>C		intron_variant	Intron 4 of 4	2		ENSP00000470582.1
CYP2B6	ENST00000598834.2	n.*652-482G>C		intron_variant	Intron 9 of 9	5		ENSP00000496294.1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39269 AN: 151790 Hom.: 6087 Cov.: 30

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.259 AC: 39277 AN: 151910 Hom.: 6088 Cov.: 30 AF XY: 0.265 AC XY: 19668 AN XY: 74220

African (AFR) AF: 0.0870 AC: 3610 AN: 41490

American (AMR) AF: 0.352 AC: 5366 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2231 AN: 5160

South Asian (SAS) AF: 0.346 AC: 1657 AN: 4794

European-Finnish (FIN) AF: 0.355 AC: 3735 AN: 10520

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20656 AN: 67914

Other (OTH) AF: 0.275 AC: 582 AN: 2114

Alfa AF: 0.170 Hom.: 389

Bravo AF: 0.254

Asia WGS AF: 0.341 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		0.69
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: rs8109848; hg19: chr19-41522069;