rs646816

Positions:

• chr19-15584290-T-G

Variant summary

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

The ENST00000593402.6(CYP4F23P):​n.1409+84T>G 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 0.0969 in 249,662 control chromosomes in the GnomAD database, including 1,358 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 0.096 (756 hom., cov: 32)
  • Exomes 𝑓: 0.098 (602 hom.)
• Consequence: CYP4F23P ENST00000593402.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

CYP4F23P (HGNC:39944): (cytochrome P450 family 4 subfamily F member 23, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 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
CYP4F23P	ENST00000593402.6	n.1409+84T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14596 AN: 152018 Hom.: 755 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0846

GnomAD4 exome AF: 0.0984 AC: 9596 AN: 97526 Hom.: 602 AF XY: 0.106 AC XY: 5851 AN XY: 55208

Gnomad4 AFR exome AF: 0.0708

Gnomad4 AMR exome AF: 0.0292

Gnomad4 ASJ exome AF: 0.0722

Gnomad4 EAS exome AF: 0.0310

Gnomad4 SAS exome AF: 0.178

Gnomad4 FIN exome AF: 0.108

Gnomad4 NFE exome AF: 0.0944

Gnomad4 OTH exome AF: 0.0896

GnomAD4 genome AF: 0.0960 AC: 14606 AN: 152136 Hom.: 756 Cov.: 32 AF XY: 0.0965 AC XY: 7178 AN XY: 74366

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.0462

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.114 Hom.: 492

Bravo AF: 0.0877

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs646816; hg19: chr19-15695101;