chr2-218787272-A-T

Position:

• chr2-218787272-A-T

Variant summary

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

The NM_000784.4(CYP27A1):​c.255+4835A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,058 control chromosomes in the GnomAD database, including 10,438 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 0.36 (10438 hom., cov: 32)
• Consequence: CYP27A1 NM_000784.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

CYP27A1 (HGNC:2605): (cytochrome P450 family 27 subfamily A 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 mitochondrial protein oxidizes cholesterol intermediates as part of the bile synthesis pathway. Since the conversion of cholesterol to bile acids is the major route for removing cholesterol from the body, this protein is important for overall cholesterol homeostasis. Mutations in this gene cause cerebrotendinous xanthomatosis, a rare autosomal recessive lipid storage disease. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP27A1	NM_000784.4	c.255+4835A>T		intron_variant		ENST00000258415.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP27A1	ENST00000258415.9	c.255+4835A>T		intron_variant		1	NM_000784.4	P1
CYP27A1	ENST00000445971.1	c.255+4835A>T		intron_variant, NMD_transcript_variant		5
CYP27A1	ENST00000466602.1	n.264+4835A>T		intron_variant, non_coding_transcript_variant		2
CYP27A1	ENST00000494263.5	n.689+4835A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54226 AN: 151940 Hom.: 10433 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.0635

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.357 AC: 54253 AN: 152058 Hom.: 10438 Cov.: 32 AF XY: 0.355 AC XY: 26416 AN XY: 74348

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.0640

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.349

Alfa AF: 0.305 Hom.: 1007

Bravo AF: 0.346

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.37

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: rs17470271; hg19: chr2-219651995;