rs1273516

Positions:

• chr19-15566899-G-A
• chr19-15566899-G-C

Variant summary

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

The variant allele was found at a frequency of 0.39 in 150,076 control chromosomes in the GnomAD database, including 11,478 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 0.39 (11478 hom., cov: 24)
• Consequence: CYP4F23P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

CYP4F23P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP4F23P		n.15566899G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP4F23P	ENST00000593402.6	n.201+2625G>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.390 AC: 58431 AN: 149962 Hom.: 11445 Cov.: 24

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.390 AC: 58514 AN: 150076 Hom.: 11478 Cov.: 24 AF XY: 0.389 AC XY: 28454 AN XY: 73168

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.405

Alfa AF: 0.405 Hom.: 14581

Bravo AF: 0.383

Asia WGS AF: 0.435 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.63
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1273516; hg19: chr19-15677710;