Genetic Variant CYP4F35P:n.1897+43618G>T (chr18-14294025-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000577614.2(CYP4F35P):n.1897+43618G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 144,030 control chromosomes in the GnomAD database, including 2,825 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 0.12 ( 2825 hom., cov: 28)

Consequence

CYP4F35P
ENST00000577614.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.784

Publications

1 publications found

Variant links:

Genes affected

CYP4F35P (HGNC:):

CYP4F35P links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577614.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CYP4F35P	ENST00000577614.2	TSL:5	n.1897+43618G>T	intron	N/A
CYP4F35P	ENST00000716198.1		n.131+30965G>T	intron	N/A
CYP4F35P	ENST00000716199.1		n.185+28357G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

17426

AN:

143912

Hom.:

2824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.0841

Gnomad ASJ

AF:

0.0612

Gnomad EAS

AF:

0.0368

Gnomad SAS

AF:

0.0534

Gnomad FIN

AF:

0.0846

Gnomad MID

AF:

0.116

Gnomad NFE

AF:

0.0989

Gnomad OTH

AF:

0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.121

AC:

17446

AN:

144030

Hom.:

2825

Cov.:

AF XY:

0.119

AC XY:

8341

AN XY:

70146

show subpopulations

African (AFR)

AF:

0.200

AC:

8183

AN:

40960

American (AMR)

AF:

0.0838

AC:

1211

AN:

14448

Ashkenazi Jewish (ASJ)

AF:

0.0612

AC:

194

AN:

3168

East Asian (EAS)

AF:

0.0368

AC:

184

AN:

4994

South Asian (SAS)

AF:

0.0535

AC:

248

AN:

4638

European-Finnish (FIN)

AF:

0.0846

AC:

810

AN:

9572

Middle Eastern (MID)

AF:

0.119

AC:

AN:

268

European-Non Finnish (NFE)

AF:

0.0989

AC:

6244

AN:

63116

Other (OTH)

AF:

0.109

AC:

214

AN:

1968

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

586

1172

1757

2343

2929

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0333

Hom.:

107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.5

(source)

DANN

Benign

0.60

PhyloP100

-0.78

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over