19-40905329-C-A

Variant names:

• chr19-40905329-C-A
• rs8109507
• ENST00000651727.1:n.1058-6365C>A

Variant summary

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

The ENST00000651727.1(CYP2G1P):​n.1058-6365C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,184 control chromosomes in the GnomAD database, including 248 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 0.054 (248 hom., cov: 31)
• Consequence: CYP2G1P ENST00000651727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 0 publications found

Genes affected

CYP2G1P (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651727.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2G1P	ENST00000651727.1		n.1058-6365C>A		intron	N/A
	ENSG00000297278	ENST00000746757.1		n.100-2979C>A		intron	N/A
	ENSG00000297319	ENST00000747088.1		n.-190G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 8230 AN: 152066 Hom.: 247 Cov.: 31

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0618

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0541 AC: 8226 AN: 152184 Hom.: 248 Cov.: 31 AF XY: 0.0507 AC XY: 3774 AN XY: 74406

African (AFR) AF: 0.0530 AC: 2202 AN: 41512

American (AMR) AF: 0.0552 AC: 843 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0441 AC: 213 AN: 4826

European-Finnish (FIN) AF: 0.0159 AC: 169 AN: 10600

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0618 AC: 4203 AN: 67994

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0580 Hom.: 143

Bravo AF: 0.0564

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.23
PhyloP100		0.011

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8109507;

hg19: chr19-41411234;