Variant chr16-74713786-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024306.5(FA2H):c.*404T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 198,208 control chromosomes in the GnomAD database, including 1,210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.078 ( 1137 hom., cov: 33)

Exomes 𝑓: 0.029 ( 73 hom. )

Consequence

FA2H
NM_024306.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.939

Variant links:

Genes affected

FA2H (HGNC:21197): (fatty acid 2-hydroxylase) This gene encodes a protein that catalyzes the synthesis of 2-hydroxysphingolipids, a subset of sphingolipids that contain 2-hydroxy fatty acids. Sphingolipids play roles in many cellular processes and their structural diversity arises from modification of the hydrophobic ceramide moiety, such as by 2-hydroxylation of the N-acyl chain, and the existence of many different head groups. Mutations in this gene have been associated with leukodystrophy dysmyelinating with spastic paraparesis with or without dystonia.[provided by RefSeq, Mar 2010]

FA2H links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 16-74713786-A-T is Benign according to our data. Variant chr16-74713786-A-T is described in ClinVar as [Benign]. Clinvar id is 320481.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FA2H	NM_024306.5 linkuse as main transcript	c.*404T>A		3_prime_UTR_variant	7/7	ENST00000219368.8
FA2H	XM_011523319.3 linkuse as main transcript	c.*404T>A		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FA2H	ENST00000219368.8 linkuse as main transcript	c.*404T>A	3_prime_UTR_variant	7/7	1	NM_024306.5	P1	Q7L5A8-1
FA2H	ENST00000562145.1 linkuse as main transcript	n.1244T>A	non_coding_transcript_exon_variant	2/2	1
FA2H	ENST00000567683.5 linkuse as main transcript	c.*802T>A	3_prime_UTR_variant, NMD_transcript_variant	5/5	2

Frequencies

GnomAD3 genomes

AF:

0.0782

AC:

11902

AN:

152204

Hom.:

1132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0334

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.0655

Gnomad SAS

AF:

0.0130

Gnomad FIN

AF:

0.00678

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0203

Gnomad OTH

AF:

0.0597

GnomAD4 exome

AF:

0.0287

AC:

1319

AN:

45886

Hom.:

Cov.:

AF XY:

0.0269

AC XY:

639

AN XY:

23782

show subpopulations

Gnomad4 AFR exome

AF:

0.205

Gnomad4 AMR exome

AF:

0.0256

Gnomad4 ASJ exome

AF:

0.00653

Gnomad4 EAS exome

AF:

0.0624

Gnomad4 SAS exome

AF:

0.00646

Gnomad4 FIN exome

AF:

0.00686

Gnomad4 NFE exome

AF:

0.0177

Gnomad4 OTH exome

AF:

0.0283

GnomAD4 genome

AF:

0.0783

AC:

11921

AN:

152322

Hom.:

1137

Cov.:

AF XY:

0.0748

AC XY:

5573

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.226

Gnomad4 AMR

AF:

0.0333

Gnomad4 ASJ

AF:

0.00663

Gnomad4 EAS

AF:

0.0656

Gnomad4 SAS

AF:

0.0126

Gnomad4 FIN

AF:

0.00678

Gnomad4 NFE

AF:

0.0203

Gnomad4 OTH

AF:

0.0581

Alfa

AF:

0.00454

Hom.:

Bravo

AF:

0.0875

Asia WGS

AF:

0.0490

AC:

172

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hereditary spastic paraplegia 35

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.42

DANN

Benign

0.52

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