chr19-41025751-A-C

Position:

• chr19-41025751-A-C

Variant summary

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

The ENST00000595391.1(CYP2A7P1):​n.495T>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 0.312 in 773,298 control chromosomes in the GnomAD database, including 40,571 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 0.33 (8582 hom., cov: 31)
  • Exomes 𝑓: 0.31 (31989 hom.)
• Consequence: CYP2A7P1 ENST00000595391.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

Genes affected

CYP2A7P1 (HGNC:2612): (cytochrome P450 family 2 subfamily A member 7 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2A7P1	ENST00000595391.1	n.495T>G		non_coding_transcript_exon_variant	4/5

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49587 AN: 151610 Hom.: 8580 Cov.: 31

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.349

GnomAD3 exomes AF: 0.323 AC: 80751 AN: 250132 Hom.: 14101 AF XY: 0.322 AC XY: 43543 AN XY: 135170

Gnomad AFR exome AF: 0.417

Gnomad AMR exome AF: 0.449

Gnomad ASJ exome AF: 0.397

Gnomad EAS exome AF: 0.157

Gnomad SAS exome AF: 0.402

Gnomad FIN exome AF: 0.226

Gnomad NFE exome AF: 0.289

Gnomad OTH exome AF: 0.320

GnomAD4 exome AF: 0.309 AC: 191968 AN: 621570 Hom.: 31989 Cov.: 3 AF XY: 0.312 AC XY: 105748 AN XY: 338428

Gnomad4 AFR exome AF: 0.421

Gnomad4 AMR exome AF: 0.448

Gnomad4 ASJ exome AF: 0.397

Gnomad4 EAS exome AF: 0.150

Gnomad4 SAS exome AF: 0.401

Gnomad4 FIN exome AF: 0.226

Gnomad4 NFE exome AF: 0.290

Gnomad4 OTH exome AF: 0.312

GnomAD4 genome AF: 0.327 AC: 49614 AN: 151728 Hom.: 8582 Cov.: 31 AF XY: 0.326 AC XY: 24130 AN XY: 74102

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.352

Alfa AF: 0.298 Hom.: 2330

Bravo AF: 0.344

Asia WGS AF: 0.306 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7249735; hg19: chr19-41531656;