1-47105832-T-C

Variant names:

• chr1-47105832-T-C
• rs6675902
• NM_178134.3:c.1068-296T>C

Variant summary

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

The NM_178134.3(CYP4Z1):​c.1068-296T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,924 control chromosomes in the GnomAD database, including 15,411 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 0.43 (15411 hom., cov: 31)
• Consequence: CYP4Z1 NM_178134.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 2 publications found

Genes affected

CYP4Z1 (HGNC:20583): (cytochrome P450 family 4 subfamily Z member 1) This gene 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 gene is part of a cluster of cytochrome P450 genes on chromosome 1p33. [provided by RefSeq, Jul 2008]

CYP4A22-AS1 (HGNC:43715): (CYP4A22 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4Z1	NM_178134.3	c.1068-296T>C		intron_variant	Intron 8 of 11	ENST00000334194.4	NP_835235.1
CYP4A22-AS1	NR_189276.1	n.1115-7412A>G		intron_variant	Intron 5 of 5
CYP4A22-AS1	NR_199717.1	n.1161-7412A>G		intron_variant	Intron 5 of 5
CYP4Z1	XM_024453856.2	c.954-296T>C		intron_variant	Intron 9 of 12		XP_024309624.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4Z1	ENST00000334194.4	c.1068-296T>C		intron_variant	Intron 8 of 11	1	NM_178134.3	ENSP00000334246.3
CYP4A22-AS1	ENST00000444042.2	n.397-8655A>G		intron_variant	Intron 3 of 3	5
CYP4A22-AS1	ENST00000815597.1	n.1124-7412A>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65257 AN: 151806 Hom.: 15377 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.430 AC: 65346 AN: 151924 Hom.: 15411 Cov.: 31 AF XY: 0.442 AC XY: 32797 AN XY: 74250

African (AFR) AF: 0.503 AC: 20814 AN: 41394

American (AMR) AF: 0.429 AC: 6552 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3466

East Asian (EAS) AF: 0.961 AC: 4968 AN: 5168

South Asian (SAS) AF: 0.656 AC: 3160 AN: 4818

European-Finnish (FIN) AF: 0.409 AC: 4308 AN: 10530

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23247 AN: 67968

Other (OTH) AF: 0.417 AC: 879 AN: 2108

Alfa AF: 0.229 Hom.: 516

Bravo AF: 0.431

Asia WGS AF: 0.772 AC: 2679 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		-0.23
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: rs6675902; hg19: chr1-47571504;