Genetic Variant CYP4F35P:n.1897+43618G>A (chr18-14294025-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000577614.2(CYP4F35P):n.1897+43618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 144,086 control chromosomes in the GnomAD database, including 54 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 0.0020 ( 54 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 -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BS2

High Homozygotes in GnomAd4 at 54 gene

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>A	intron	N/A
CYP4F35P	ENST00000716198.1		n.131+30965G>A	intron	N/A
CYP4F35P	ENST00000716199.1		n.185+28357G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00201

AC:

289

AN:

143968

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000709

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000970

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000646

Gnomad FIN

AF:

0.000522

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00374

Gnomad OTH

AF:

0.00103

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

GnomAD4 genome

AF:

0.00201

AC:

290

AN:

144086

Hom.:

Cov.:

AF XY:

0.00175

AC XY:

123

AN XY:

70180

show subpopulations

African (AFR)

AF:

0.000707

AC:

AN:

41000

American (AMR)

AF:

0.000969

AC:

AN:

14452

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3168

East Asian (EAS)

AF:

0.00

AC:

AN:

4996

South Asian (SAS)

AF:

0.000862

AC:

AN:

4642

European-Finnish (FIN)

AF:

0.000522

AC:

AN:

9572

Middle Eastern (MID)

AF:

0.00

AC:

AN:

268

European-Non Finnish (NFE)

AF:

0.00374

AC:

236

AN:

63122

Other (OTH)

AF:

0.00102

AC:

AN:

1968

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.000652

Hom.:

107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

2.0

(source)

DANN

Benign

0.69

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