Menu
GeneBe

rs7249735

Positions:

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

2

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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP2A7P1ENST00000595391.1 linkuse as main transcriptn.495T>G non_coding_transcript_exon_variant 4/5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.327
AC:
49587
AN:
151610
Hom.:
8580
Cov.:
31
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.:
3
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.327
AC:
49614
AN:
151728
Hom.:
8582
Cov.:
31
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.

Other links and lift over

dbSNP: rs7249735; hg19: chr19-41531656; API