Variant 3-128909970-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001394090.1(CFAP92):c.*329C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 1,605,254 control chromosomes in the GnomAD database, including 209 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.011 ( 14 hom., cov: 33)

Exomes 𝑓: 0.016 ( 195 hom. )

Consequence

CFAP92
NM_001394090.1 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.348

Variant links:

Genes affected

CFAP92 (HGNC:29231): (cilia and flagella associated protein 92 (putative))

CFAP92 links:

ACAD9 (HGNC:21497): (acyl-CoA dehydrogenase family member 9) This gene encodes a member of the acyl-CoA dehydrogenase family. Members of this family of proteins localize to the mitochondria and catalyze the rate-limiting step in the beta-oxidation of fatty acyl-CoA. The encoded protein is specifically active toward palmitoyl-CoA and long-chain unsaturated substrates. Mutations in this gene cause acyl-CoA dehydrogenase family member type 9 deficiency. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2010]

ACAD9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 3-128909970-G-A is Benign according to our data. Variant chr3-128909970-G-A is described in ClinVar as [Benign]. Clinvar id is 2654113.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0113 (1717/152360) while in subpopulation NFE AF= 0.0174 (1185/68032). AF 95% confidence interval is 0.0166. There are 14 homozygotes in gnomad4. There are 801 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP92	NM_001394090.1 linkuse as main transcript	c.*329C>T		3_prime_UTR_variant	16/16	ENST00000645291.3	NP_001381019.1
ACAD9	NM_014049.5 linkuse as main transcript	c.1564-51G>A		intron_variant		ENST00000308982.12	NP_054768.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP92	ENST00000645291.3 linkuse as main transcript	c.*329C>T		3_prime_UTR_variant	16/16		NM_001394090.1	ENSP00000496592	P2
ACAD9	ENST00000308982.12 linkuse as main transcript	c.1564-51G>A		intron_variant		1	NM_014049.5	ENSP00000312618	P1

Frequencies

GnomAD3 genomes

AF:

0.0113

AC:

1717

AN:

152242

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00311

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00805

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00786

Gnomad FIN

AF:

0.0190

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0174

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.0122

AC:

2885

AN:

235516

Hom.:

AF XY:

0.0128

AC XY:

1614

AN XY:

126584

show subpopulations

Gnomad AFR exome

AF:

0.00255

Gnomad AMR exome

AF:

0.00546

Gnomad ASJ exome

AF:

0.00406

Gnomad EAS exome

AF:

0.0000578

Gnomad SAS exome

AF:

0.0106

Gnomad FIN exome

AF:

0.0182

Gnomad NFE exome

AF:

0.0177

Gnomad OTH exome

AF:

0.0126

GnomAD4 exome

AF:

0.0160

AC:

23220

AN:

1452894

Hom.:

195

Cov.:

AF XY:

0.0158

AC XY:

11379

AN XY:

721716

show subpopulations

Gnomad4 AFR exome

AF:

0.00251

Gnomad4 AMR exome

AF:

0.00555

Gnomad4 ASJ exome

AF:

0.00504

Gnomad4 EAS exome

AF:

0.0000507

Gnomad4 SAS exome

AF:

0.0106

Gnomad4 FIN exome

AF:

0.0185

Gnomad4 NFE exome

AF:

0.0180

Gnomad4 OTH exome

AF:

0.0152

GnomAD4 genome

AF:

0.0113

AC:

1717

AN:

152360

Hom.:

Cov.:

AF XY:

0.0108

AC XY:

801

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00310

Gnomad4 AMR

AF:

0.00804

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00786

Gnomad4 FIN

AF:

0.0190

Gnomad4 NFE

AF:

0.0174

Gnomad4 OTH

AF:

0.00805

Alfa

AF:

0.00787

Hom.:

Bravo

AF:

0.00965

Asia WGS

AF:

0.00433

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2023

ACAD9: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.20

DANN

Benign

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over