GeneBe

chr19-41025463-T-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 25)
Exomes 𝑓: 0.0000022 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CYP2A7P1
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Publications

12 publications found
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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYP2A7P1 n.41025463T>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CYP2A7P1ENST00000595391.1 linkn.646+137A>T intron_variant Intron 4 of 4 6

Frequencies

GnomAD3 genomes
Cov.:
25
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000217
AC:
1
AN:
460326
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
247366
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
14192
American (AMR)
AF:
0.0000322
AC:
1
AN:
31086
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15626
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26772
South Asian (SAS)
AF:
0.00
AC:
0
AN:
54084
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
28962
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2174
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
261900
Other (OTH)
AF:
0.00
AC:
0
AN:
25530
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.34
DANN
Benign
0.19
PhyloP100
-0.054

Splicing

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

Publications

Other links and lift over

dbSNP: rs11666982; hg19: chr19-41531368; API