rs76478271

chr19-40819294-T-A

Variant summary

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

The ENST00000437853.1(CYP2F2P):n.874-391A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,000 control chromosomes in the GnomAD database, including 3,955 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 0.15 (3955 hom., cov: 30)
• Consequence: CYP2F2P ENST00000437853.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

CYP2F2P (HGNC:18851): (cytochrome P450 family 2 subfamily F member 2, pseudogene)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2F2P	ENST00000437853.1	n.874-391A>T		intron_variant, non_coding_transcript_variant
	ENST00000641827.1	n.519-395A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23032 AN: 150880 Hom.: 3936 Cov.: 30

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0343

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.153 AC: 23088 AN: 151000 Hom.: 3955 Cov.: 30 AF XY: 0.146 AC XY: 10779 AN XY: 73690

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.0908

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.00118

Gnomad4 SAS AF: 0.0344

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.151

Alfa AF: 0.116 Hom.: 290

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.31
Dann	Benign	0.23

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: rs76478271; hg19: chr19-41325199;