Variant rs41272317 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_032169.5(ACAD11):c.1414+1G>T variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,579,782 control chromosomes in the GnomAD database, including 526 homozygotes. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.021 ( 57 hom., cov: 32)

Exomes 𝑓: 0.019 ( 469 hom. )

Consequence

ACAD11
NM_032169.5 splice_donor, intron

Scores

Splicing: ADA: 1.000

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.77

Variant links:

Genes affected

ACAD11 (HGNC:30211): (acyl-CoA dehydrogenase family member 11) This gene encodes an acyl-CoA dehydrogenase enzyme with a preference for carbon chain lengths between 20 and 26. Naturally occurring read-through transcription occurs between the upstream gene NPHP3 (nephronophthisis 3 (adolescent)) and this gene. [provided by RefSeq, Aug 2015]

ACAD11 links:

ACAD11 (HGNC:):

ACAD11 links:

NPHP3-ACAD11 (HGNC:48351): (NPHP3-ACAD11 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring NPHP3 (nephronophthisis 3, adolescent) and ACAD11 (acyl-CoA dehydrogenase family, member 11) genes on chromosome 3. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

NPHP3-ACAD11 links:

ACKR4 (HGNC:1611): (atypical chemokine receptor 4) The protein encoded by this gene is a member of the G protein-coupled receptor family, and is a receptor for C-C type chemokines. This receptor has been shown to bind dendritic cell- and T cell-activated chemokines including CCL19/ELC, CCL21/SLC, and CCL25/TECK. A pseudogene of this gene is found on chromosome 6. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2013]

ACKR4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACAD11	NM_032169.5 linkuse as main transcript	c.1414+1G>T		splice_donor_variant, intron_variant		ENST00000264990.11	NP_115545.3	Q709F0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACAD11	ENST00000264990.11 linkuse as main transcript	c.1414+1G>T		splice_donor_variant, intron_variant		1	NM_032169.5	ENSP00000264990.6		Q709F0-1

Frequencies

GnomAD3 genomes

AF:

0.0214

AC:

3250

AN:

152034

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0275

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00957

Gnomad ASJ

AF:

0.0196

Gnomad EAS

AF:

0.0672

Gnomad SAS

AF:

0.0715

Gnomad FIN

AF:

0.00605

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0159

Gnomad OTH

AF:

0.0248

GnomAD3 exomes

AF:

0.0239

AC:

5353

AN:

224206

Hom.:

121

AF XY:

0.0262

AC XY:

3195

AN XY:

122122

show subpopulations

Gnomad AFR exome

AF:

0.0261

Gnomad AMR exome

AF:

0.00717

Gnomad ASJ exome

AF:

0.0222

Gnomad EAS exome

AF:

0.0675

Gnomad SAS exome

AF:

0.0691

Gnomad FIN exome

AF:

0.00613

Gnomad NFE exome

AF:

0.0144

Gnomad OTH exome

AF:

0.0176

GnomAD4 exome

AF:

0.0191

AC:

27253

AN:

1427630

Hom.:

469

Cov.:

AF XY:

0.0204

AC XY:

14474

AN XY:

709992

show subpopulations

Gnomad4 AFR exome

AF:

0.0291

Gnomad4 AMR exome

AF:

0.00798

Gnomad4 ASJ exome

AF:

0.0206

Gnomad4 EAS exome

AF:

0.0441

Gnomad4 SAS exome

AF:

0.0665

Gnomad4 FIN exome

AF:

0.00655

Gnomad4 NFE exome

AF:

0.0153

Gnomad4 OTH exome

AF:

0.0218

GnomAD4 genome

AF:

0.0214

AC:

3257

AN:

152152

Hom.:

Cov.:

AF XY:

0.0218

AC XY:

1623

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.0276

Gnomad4 AMR

AF:

0.00949

Gnomad4 ASJ

AF:

0.0196

Gnomad4 EAS

AF:

0.0670

Gnomad4 SAS

AF:

0.0718

Gnomad4 FIN

AF:

0.00605

Gnomad4 NFE

AF:

0.0159

Gnomad4 OTH

AF:

0.0255

Alfa

AF:

0.0177

Hom.:

Bravo

AF:

0.0210

TwinsUK

AF:

0.0138

AC:

ALSPAC

AF:

0.0187

AC:

ESP6500AA

AF:

0.0259

AC:

114

ESP6500EA

AF:

0.0155

AC:

133

ExAC

AF:

0.0255

AC:

3096

Asia WGS

AF:

0.0580

AC:

202

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.089

BayesDel_noAF

Benign

-0.27

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Pathogenic

1.2

Eigen_PC

Pathogenic

1.0

FATHMM_MKL

Pathogenic

0.98

ClinPred

0.028

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.94

SpliceAI score (max)

0.91

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.91

Position offset: 1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over