1-47002797-C-T

Variant names:

• chr1-47002797-C-T
• rs6669062
• NM_001320289.2:c.175-27193C>T

Variant summary

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

The NM_001320289.2(CYP4X1):​c.175-27193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,130 control chromosomes in the GnomAD database, including 4,991 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 0.24 (4991 hom., cov: 32)
• Consequence: CYP4X1 NM_001320289.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 0 publications found

Genes affected

CYP4X1 (HGNC:20244): (cytochrome P450 family 4 subfamily X member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes and is located within a cluster of genes belonging to this superfamily on chromosome 1. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. The expression pattern of a similar rat protein suggests that this protein may be involved in neurovascular function in the brain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

CYP4A44P (HGNC:42416): (cytochrome P450 family 4 subfamily A member 44, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320289.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4X1	NM_001320289.2		c.175-27193C>T		intron	N/A	NP_001307218.1	Q8N118-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP4A44P	ENST00000569984.1	TSL:6	n.*198G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37229 AN: 152012 Hom.: 4991 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.245 AC: 37233 AN: 152130 Hom.: 4991 Cov.: 32 AF XY: 0.252 AC XY: 18768 AN XY: 74342

African (AFR) AF: 0.169 AC: 7031 AN: 41520

American (AMR) AF: 0.281 AC: 4290 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3466

East Asian (EAS) AF: 0.512 AC: 2647 AN: 5170

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4824

European-Finnish (FIN) AF: 0.301 AC: 3181 AN: 10560

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16893 AN: 68000

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.241 Hom.: 1031

Bravo AF: 0.234

Asia WGS AF: 0.402 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.33
DANN	Benign	0.39
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6669062; hg19: chr1-47468469;