Variant rs3734120 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_205836.3(FBXO38):c.3389-63C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,423,262 control chromosomes in the GnomAD database, including 50,903 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5334 hom., cov: 32)

Exomes 𝑓: 0.27 ( 45569 hom. )

Consequence

FBXO38
NM_205836.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.489

Variant links:

Genes affected

FBXO38 (HGNC:28844): (F-box protein 38) This gene encodes a large protein that contains an F-box domain and may participate in protein ubiquitination. The encoded protein is a transcriptional co-activator of Krueppel-like factor 7 (Klf7). A heterozygous mutation in this gene was found in individuals with autosomal dominant distal hereditary motor neuronopathy type IID. There is a pseudogene for this gene on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

FBXO38 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=-0.74).

BP6

Variant 5-148441906-C-T is Benign according to our data. Variant chr5-148441906-C-T is described in ClinVar as [Benign]. Clinvar id is 1250411.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBXO38	NM_205836.3 linkuse as main transcript	c.3389-63C>T		intron_variant		ENST00000340253.10	NP_995308.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
FBXO38	ENST00000340253.10 linkuse as main transcript	c.3389-63C>T	intron_variant	5	NM_205836.3	ENSP00000342023.6	Q6PIJ6-1
FBXO38	ENST00000394370.7 linkuse as main transcript	c.3164-63C>T	intron_variant	1		ENSP00000377895.3	Q6PIJ6-2
FBXO38	ENST00000513826.1 linkuse as main transcript	c.2654-63C>T	intron_variant	1		ENSP00000426410.1	Q6PIJ6-3
FBXO38	ENST00000296701.10 linkuse as main transcript	c.2654-63C>T	intron_variant	2		ENSP00000296701.6	Q6PIJ6-3

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

40012

AN:

151966

Hom.:

5323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.289

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.250

GnomAD4 exome

AF:

0.266

AC:

337932

AN:

1271184

Hom.:

45569

AF XY:

0.267

AC XY:

168729

AN XY:

633068

show subpopulations

Gnomad4 AFR exome

AF:

0.276

Gnomad4 AMR exome

AF:

0.281

Gnomad4 ASJ exome

AF:

0.191

Gnomad4 EAS exome

AF:

0.196

Gnomad4 SAS exome

AF:

0.292

Gnomad4 FIN exome

AF:

0.234

Gnomad4 NFE exome

AF:

0.269

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.263

AC:

40052

AN:

152078

Hom.:

5334

Cov.:

AF XY:

0.260

AC XY:

19335

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.274

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.288

Gnomad4 FIN

AF:

0.228

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.248

Alfa

AF:

0.265

Hom.:

1112

Bravo

AF:

0.264

Asia WGS

AF:

0.257

AC:

894

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

GeneDx

Mar 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

6.1

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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