Variant 1-154983399-TGA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_201398.3(FLAD1):c.-145+6_-145+7delAG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0042 in 286,006 control chromosomes in the GnomAD database, including 6 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 2 hom., cov: 31)

Exomes 𝑓: 0.0047 ( 4 hom. )

Consequence

FLAD1
NM_201398.3 splice_region, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.86

Variant links:

Genes affected

FLAD1 (HGNC:24671): (flavin adenine dinucleotide synthetase 1) This gene encodes the enzyme that catalyzes adenylation of flavin mononucleotide (FMN) to form flavin adenine dinucleotide (FAD) coenzyme. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

FLAD1 links:

FLAD1 (HGNC:):

FLAD1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-154983399-TGA-T is Benign according to our data. Variant chr1-154983399-TGA-T is described in ClinVar as [Likely_benign]. Clinvar id is 419775.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-154983399-TGA-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00373 (567/151872) while in subpopulation SAS AF= 0.0169 (81/4796). AF 95% confidence interval is 0.0139. There are 2 homozygotes in gnomad4. There are 284 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLAD1	NM_025207.5 linkuse as main transcript	c.-292_-291delAG		5_prime_UTR_variant	1/7	ENST00000292180.8	NP_079483.3	Q8NFF5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLAD1	ENST00000292180 linkuse as main transcript	c.-292_-291delAG		5_prime_UTR_variant	1/7	1	NM_025207.5	ENSP00000292180.3		Q8NFF5-1

Frequencies

GnomAD3 genomes

AF:

0.00374

AC:

568

AN:

151758

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000775

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.00302

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.000388

Gnomad SAS

AF:

0.0169

Gnomad FIN

AF:

0.000757

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00487

Gnomad OTH

AF:

0.00336

GnomAD4 exome

AF:

0.00473

AC:

635

AN:

134134

Hom.:

AF XY:

0.00479

AC XY:

329

AN XY:

68750

show subpopulations

Gnomad4 AFR exome

AF:

0.000626

Gnomad4 AMR exome

AF:

0.00161

Gnomad4 ASJ exome

AF:

0.00800

Gnomad4 EAS exome

AF:

0.000265

Gnomad4 SAS exome

AF:

0.0145

Gnomad4 FIN exome

AF:

0.000529

Gnomad4 NFE exome

AF:

0.00521

Gnomad4 OTH exome

AF:

0.00537

GnomAD4 genome

AF:

0.00373

AC:

567

AN:

151872

Hom.:

Cov.:

AF XY:

0.00383

AC XY:

284

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.000748

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.0101

Gnomad4 EAS

AF:

0.000389

Gnomad4 SAS

AF:

0.0169

Gnomad4 FIN

AF:

0.000757

Gnomad4 NFE

AF:

0.00488

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00362

Hom.:

Bravo

AF:

0.00362

Asia WGS

AF:

0.00375

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 01, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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