Variant chr10-119141113-C-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_213649.2(SFXN4):c.*129G>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 0.0286 in 628,966 control chromosomes in the GnomAD database, including 1,150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 554 hom., cov: 32)

Exomes 𝑓: 0.021 ( 596 hom. )

Consequence

SFXN4
NM_213649.2 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.30

Variant links:

Genes affected

SFXN4 (HGNC:16088): (sideroflexin 4) This gene encodes a member of the sideroflexin family. The encoded protein is a transmembrane protein of the inner mitochondrial membrane, and is required for mitochondrial respiratory homeostasis and erythropoiesis. Mutations in this gene are associated with mitochondriopathy and macrocytic anemia. Alternatively spliced transcript variants have been found in this gene. [provided by RefSeq, Jan 2014]

SFXN4 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=-0.93).

BP6

Variant 10-119141113-C-T is Benign according to our data. Variant chr10-119141113-C-T is described in ClinVar as [Benign]. Clinvar id is 1237656.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFXN4	NM_213649.2 linkuse as main transcript	c.*129G>A		3_prime_UTR_variant	14/14	ENST00000355697.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFXN4	ENST00000355697.7 linkuse as main transcript	c.*129G>A	3_prime_UTR_variant	14/14	1	NM_213649.2	P1	Q6P4A7-1
SFXN4	ENST00000484960.5 linkuse as main transcript	n.355G>A	non_coding_transcript_exon_variant	3/3	3
SFXN4	ENST00000490417.6 linkuse as main transcript	n.606G>A	non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes

AF:

0.0537

AC:

8169

AN:

152006

Hom.:

552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0650

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.0195

Gnomad FIN

AF:

0.000659

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00104

Gnomad OTH

AF:

0.0378

GnomAD4 exome

AF:

0.0205

AC:

9784

AN:

476842

Hom.:

596

Cov.:

AF XY:

0.0185

AC XY:

4761

AN XY:

257002

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.0879

Gnomad4 ASJ exome

AF:

0.000459

Gnomad4 EAS exome

AF:

0.156

Gnomad4 SAS exome

AF:

0.0150

Gnomad4 FIN exome

AF:

0.000740

Gnomad4 NFE exome

AF:

0.000968

Gnomad4 OTH exome

AF:

0.0238

GnomAD4 genome

AF:

0.0539

AC:

8194

AN:

152124

Hom.:

554

Cov.:

AF XY:

0.0539

AC XY:

4008

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.145

Gnomad4 AMR

AF:

0.0649

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.179

Gnomad4 SAS

AF:

0.0193

Gnomad4 FIN

AF:

0.000659

Gnomad4 NFE

AF:

0.00104

Gnomad4 OTH

AF:

0.0379

Alfa

AF:

0.0176

Hom.:

157

Bravo

AF:

0.0664

Asia WGS

AF:

0.0790

AC:

274

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.031

DANN

Benign

0.50

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