19-15566899-G-A

Variant names:

• chr19-15566899-G-A
• rs1273516

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYP4F23P		n.15566899G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F23P	ENST00000593402.6	n.201+2625G>A		intron_variant	Intron 1 of 11	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

African (AFR) AF: 0.397 AC: 16124 AN: 40574

American (AMR) AF: 0.281 AC: 4224 AN: 15038

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1751 AN: 3456

East Asian (EAS) AF: 0.449 AC: 2234 AN: 4978

South Asian (SAS) AF: 0.437 AC: 2060 AN: 4714

European-Finnish (FIN) AF: 0.372 AC: 3866 AN: 10398

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27013 AN: 67644

Other (OTH) AF: 0.405 AC: 839 AN: 2074

Alfa AF: 0.402 Hom.: 27151

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1273516; hg19: chr19-15677710;