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GeneBe

rs17756963

Variant summary

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

The ENST00000589847.3(CYP4F9P):n.646G>C 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 0.173 in 222,750 control chromosomes in the GnomAD database, including 4,904 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 0.19 ( 3868 hom., cov: 32)
Exomes 𝑓: 0.14 ( 1036 hom. )

Consequence

CYP4F9P
ENST00000589847.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112
Variant links:
Genes affected
CYP4F9P (HGNC:39940): (cytochrome P450 family 4 subfamily F member 9, pseudogene)

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=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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
CYP4F9PENST00000589847.3 linkuse as main transcriptn.646G>C non_coding_transcript_exon_variant 6/12

Frequencies

GnomAD3 genomes
AF:
0.186
AC:
28348
AN:
152010
Hom.:
3856
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.355
Gnomad AMI
AF:
0.142
Gnomad AMR
AF:
0.131
Gnomad ASJ
AF:
0.120
Gnomad EAS
AF:
0.449
Gnomad SAS
AF:
0.177
Gnomad FIN
AF:
0.132
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.0902
Gnomad OTH
AF:
0.172
GnomAD4 exome
AF:
0.144
AC:
10175
AN:
70620
Hom.:
1036
Cov.:
0
AF XY:
0.137
AC XY:
5533
AN XY:
40430
show subpopulations
Gnomad4 AFR exome
AF:
0.368
Gnomad4 AMR exome
AF:
0.141
Gnomad4 ASJ exome
AF:
0.103
Gnomad4 EAS exome
AF:
0.459
Gnomad4 SAS exome
AF:
0.173
Gnomad4 FIN exome
AF:
0.140
Gnomad4 NFE exome
AF:
0.0938
Gnomad4 OTH exome
AF:
0.128
GnomAD4 genome
AF:
0.187
AC:
28403
AN:
152130
Hom.:
3868
Cov.:
32
AF XY:
0.187
AC XY:
13882
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.355
Gnomad4 AMR
AF:
0.131
Gnomad4 ASJ
AF:
0.120
Gnomad4 EAS
AF:
0.450
Gnomad4 SAS
AF:
0.176
Gnomad4 FIN
AF:
0.132
Gnomad4 NFE
AF:
0.0903
Gnomad4 OTH
AF:
0.174
Alfa
AF:
0.0329
Hom.:
27
Bravo
AF:
0.195
Asia WGS
AF:
0.350
AC:
1218
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.97
Dann
Benign
0.43

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: rs17756963; hg19: chr19-16102980; API