19-40898291-A-G

Position:

• chr19-40898291-A-G

Variant summary

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

The NR_040249.1(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 NR_040249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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/exons	MANE	UniProt
CYP2G1P	NR_040249.1	n.1800A>G		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2G1P	ENST00000597833.3	n.645A>G		non_coding_transcript_exon_variant	4/6
CYP2G1P	ENST00000651727.1	n.1057+4299A>G		intron_variant, non_coding_transcript_variant
CYP2G1P	ENST00000252909.8	n.1800A>G		non_coding_transcript_exon_variant	3/5	2

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

GnomAD3 exomes AF: 0.539 AC: 74364 AN: 138004 Hom.: 20618 AF XY: 0.538 AC XY: 40186 AN XY: 74742

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 SAS exome AF: 0.585

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

Gnomad4 AFR exome AF: 0.566

Gnomad4 AMR exome AF: 0.682

Gnomad4 ASJ exome AF: 0.430

Gnomad4 EAS exome AF: 0.465

Gnomad4 SAS exome AF: 0.582

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.490

Gnomad4 OTH exome AF: 0.494

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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.533

Alfa AF: 0.505 Hom.: 5435

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10419393; hg19: chr19-41404196;