19-41025463-T-G

Variant summary

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

The ENST00000595391.1(CYP2A7P1):n.646+137A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 610,374 control chromosomes in the GnomAD database, including 93,093 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 0.58 (27899 hom., cov: 25)
  • Exomes 𝑓: 0.52 (65194 hom.)
• Consequence: CYP2A7P1 ENST00000595391.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2A7P1	ENST00000595391.1	n.646+137A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.583 AC: 87576 AN: 150290 Hom.: 27867 Cov.: 25

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.595

GnomAD4 exome AF: 0.520 AC: 239055 AN: 459964 Hom.: 65194 AF XY: 0.523 AC XY: 129291 AN XY: 247162

Gnomad4 AFR exome AF: 0.836

Gnomad4 AMR exome AF: 0.741

Gnomad4 ASJ exome AF: 0.612

Gnomad4 EAS exome AF: 0.413

Gnomad4 SAS exome AF: 0.617

Gnomad4 FIN exome AF: 0.453

Gnomad4 NFE exome AF: 0.466

Gnomad4 OTH exome AF: 0.535

GnomAD4 genome AF: 0.583 AC: 87660 AN: 150410 Hom.: 27899 Cov.: 25 AF XY: 0.585 AC XY: 42911 AN XY: 73342

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.595

Alfa AF: 0.474 Hom.: 34601

Bravo AF: 0.611

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.37
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11666982; hg19: chr19-41531368;