chr19-40891756-C-A

Position:

• chr19-40891756-C-A

Variant summary

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

The NR_040249.1(CYP2G1P):​n.931C>A 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 0.756 in 345,904 control chromosomes in the GnomAD database, including 99,315 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 0.77 (45330 hom., cov: 31)
  • Exomes 𝑓: 0.74 (53985 hom.)
• Consequence: CYP2G1P NR_040249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP2G1P	NR_040249.1	n.931C>A		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2G1P	ENST00000597833.3	n.181-235C>A		intron_variant, non_coding_transcript_variant
CYP2G1P	ENST00000252909.8	n.931C>A		non_coding_transcript_exon_variant	1/5	2

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117159 AN: 151934 Hom.: 45286 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.754

GnomAD4 exome AF: 0.743 AC: 144088 AN: 193852 Hom.: 53985 Cov.: 0 AF XY: 0.743 AC XY: 73221 AN XY: 98520

Gnomad4 AFR exome AF: 0.803

Gnomad4 AMR exome AF: 0.790

Gnomad4 ASJ exome AF: 0.745

Gnomad4 EAS exome AF: 0.624

Gnomad4 SAS exome AF: 0.736

Gnomad4 FIN exome AF: 0.835

Gnomad4 NFE exome AF: 0.745

Gnomad4 OTH exome AF: 0.744

GnomAD4 genome AF: 0.771 AC: 117261 AN: 152052 Hom.: 45330 Cov.: 31 AF XY: 0.774 AC XY: 57565 AN XY: 74326

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.754

Alfa AF: 0.758 Hom.: 46758

Bravo AF: 0.768

Asia WGS AF: 0.706 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8103444; hg19: chr19-41397661;