NM_001367502.1:c.473+983A>T

Variant names:

• chr2-127204917-T-A
• rs7585314
• NM_001367502.1:c.473+983A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367502.1(CYP27C1):​c.473+983A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CYP27C1 NM_001367502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

Genes affected

CYP27C1 (HGNC:33480): (cytochrome P450 family 27 subfamily C 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. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP27C1	NM_001367502.1	c.473+983A>T		intron_variant	Intron 2 of 8	ENST00000664447.2	NP_001354431.1
CYP27C1	NM_001001665.4	c.-23+742A>T		intron_variant	Intron 1 of 7		NP_001001665.3
CYP27C1	NM_001367501.1	c.-22-1346A>T		intron_variant	Intron 1 of 7		NP_001354430.1
CYP27C1	XM_024452838.2	c.110+983A>T		intron_variant	Intron 2 of 8		XP_024308606.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP27C1	ENST00000664447.2	c.473+983A>T		intron_variant	Intron 2 of 8		NM_001367502.1	ENSP00000499243.1
CYP27C1	ENST00000335247.11	c.-23+742A>T		intron_variant	Intron 1 of 7	1		ENSP00000334128.7
CYP27C1	ENST00000409327.2	c.-22-1346A>T		intron_variant	Intron 1 of 7	2		ENSP00000387198.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7585314; hg19: chr2-127962493;