chr19-40898291-A-G

Variant names:

• chr19-40898291-A-G
• rs10419393
• ENST00000252909.8:n.1800A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000252909.8(CYP2G1P):​n.1800A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 456,226 control chromosomes in the GnomAD database, including 63,677 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 0.52 (21151 hom., cov: 29)
  • Exomes 𝑓: 0.52 (42526 hom.)
• Consequence: CYP2G1P ENST00000252909.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 12 publications found

Genes affected

CYP2G1P (HGNC:):

CYP2G1P (HGNC:2633): (cytochrome P450 family 2 subfamily G member 1, pseudogene) Predicted to enable heme binding activity and monooxygenase activity. Predicted to be involved in epoxygenase P450 pathway and xenobiotic catabolic process. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.012).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2G1P	NR_040249.1	n.1800A>G		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268797	ENST00000601627.1	n.*384A>G		downstream_gene_variant		3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79383 AN: 151568 Hom.: 21141 Cov.: 29

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.532

GnomAD2 exomes AF: 0.539 AC: 74364 AN: 138004 AF XY: 0.538

Gnomad AFR exome AF: 0.572

Gnomad AMR exome AF: 0.682

Gnomad ASJ exome AF: 0.435

Gnomad EAS exome AF: 0.462

Gnomad FIN exome AF: 0.445

Gnomad NFE exome AF: 0.498

Gnomad OTH exome AF: 0.493

GnomAD4 exome AF: 0.523 AC: 159222 AN: 304538 Hom.: 42526 Cov.: 0 AF XY: 0.525 AC XY: 91040 AN XY: 173348

African (AFR) AF: 0.566 AC: 4881 AN: 8630

American (AMR) AF: 0.682 AC: 18606 AN: 27280

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 4635 AN: 10784

East Asian (EAS) AF: 0.465 AC: 4286 AN: 9208

South Asian (SAS) AF: 0.582 AC: 34763 AN: 59720

European-Finnish (FIN) AF: 0.444 AC: 5728 AN: 12910

Middle Eastern (MID) AF: 0.481 AC: 1336 AN: 2780

European-Non Finnish (NFE) AF: 0.490 AC: 77916 AN: 158926

Other (OTH) AF: 0.494 AC: 7071 AN: 14300

GnomAD4 genome AF: 0.524 AC: 79442 AN: 151688 Hom.: 21151 Cov.: 29 AF XY: 0.523 AC XY: 38749 AN XY: 74080

African (AFR) AF: 0.566 AC: 23388 AN: 41320

American (AMR) AF: 0.626 AC: 9545 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2281 AN: 5126

South Asian (SAS) AF: 0.597 AC: 2865 AN: 4800

European-Finnish (FIN) AF: 0.429 AC: 4501 AN: 10488

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33721 AN: 67932

Other (OTH) AF: 0.533 AC: 1123 AN: 2106

Alfa AF: 0.511 Hom.: 9595

Bravo AF: 0.538

Asia WGS AF: 0.522 AC: 1817 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	5.2
DANN	Benign	0.25
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs10419393; hg19: chr19-41404196; COSMIC: COSV107263839;