rs7687961

chr4-186200855-C-Achr4-186200855-C-G

Variant summary

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

The NM_207352.4(CYP4V2):c.802-302C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,958 control chromosomes in the GnomAD database, including 40,277 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 0.72 (40277 hom., cov: 32)
• Consequence: CYP4V2 NM_207352.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562

Genes affected

CYP4V2 (HGNC:23198): (cytochrome P450 family 4 subfamily V member 2) This gene encodes a member of the cytochrome P450 hemethiolate protein superfamily which are involved in oxidizing various substrates in the metabolic pathway. It is implicated in the metabolism of fatty acid precursors into n-3 polyunsaturated fatty acids. Mutations in this gene result in Bietti crystalline corneoretinal dystrophy. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP4V2	NM_207352.4	c.802-302C>A		intron_variant		ENST00000378802.5
CYP4V2	XM_005262935.5	c.802-302C>A		intron_variant
CYP4V2	XM_047450077.1	c.406-302C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP4V2	ENST00000378802.5	c.802-302C>A		intron_variant		1	NM_207352.4	P1
CYP4V2	ENST00000507209.5	n.1643-302C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109447 AN: 151840 Hom.: 40260 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.721 AC: 109508 AN: 151958 Hom.: 40277 Cov.: 32 AF XY: 0.720 AC XY: 53434 AN XY: 74262

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.752

Alfa AF: 0.786 Hom.: 80230

Bravo AF: 0.704

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.2
Dann	Benign	0.29

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: rs7687961; hg19: chr4-187122009;