Variant rs7249735 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.97

Variant links:

Genes affected

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

CYP2A7P1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 linkuse as main transcript	n.495T>G		non_coding_transcript_exon_variant	4/5

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49587

AN:

151610

Hom.:

8580

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.312

AC XY:

105748

AN XY:

338428

show subpopulations

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.:

AF XY:

0.326

AC XY:

24130

AN XY:

74102

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over