Variant rs2275112 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.361-42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,589,208 control chromosomes in the GnomAD database, including 98,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7566 hom., cov: 32)

Exomes 𝑓: 0.35 ( 90593 hom. )

Consequence

SFXN4
NM_213649.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0650

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:

SFXN4 (HGNC:):

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=-0.81).

BP6

Variant 10-119158104-G-A is Benign according to our data. Variant chr10-119158104-G-A is described in ClinVar as [Benign]. Clinvar id is 1292078.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFXN4	NM_213649.2 linkuse as main transcript	c.361-42C>T		intron_variant		ENST00000355697.7	NP_998814.1	Q6P4A7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFXN4	ENST00000355697.7 linkuse as main transcript	c.361-42C>T		intron_variant		1	NM_213649.2	ENSP00000347924.2		Q6P4A7-1

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45456

AN:

151926

Hom.:

7569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.403

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.457

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.308

GnomAD3 exomes

AF:

0.332

AC:

83235

AN:

251032

Hom.:

14641

AF XY:

0.340

AC XY:

46150

AN XY:

135782

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.282

Gnomad ASJ exome

AF:

0.307

Gnomad EAS exome

AF:

0.159

Gnomad SAS exome

AF:

0.397

Gnomad FIN exome

AF:

0.457

Gnomad NFE exome

AF:

0.359

Gnomad OTH exome

AF:

0.336

GnomAD4 exome

AF:

0.351

AC:

504415

AN:

1437162

Hom.:

90593

Cov.:

AF XY:

0.353

AC XY:

253143

AN XY:

716510

show subpopulations

Gnomad4 AFR exome

AF:

0.161

Gnomad4 AMR exome

AF:

0.286

Gnomad4 ASJ exome

AF:

0.306

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.401

Gnomad4 FIN exome

AF:

0.456

Gnomad4 NFE exome

AF:

0.358

Gnomad4 OTH exome

AF:

0.325

GnomAD4 genome

AF:

0.299

AC:

45453

AN:

152046

Hom.:

7566

Cov.:

AF XY:

0.304

AC XY:

22587

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.286

Gnomad4 ASJ

AF:

0.303

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.390

Gnomad4 FIN

AF:

0.457

Gnomad4 NFE

AF:

0.362

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.331

Hom.:

1896

Bravo

AF:

0.274

Asia WGS

AF:

0.304

AC:

1055

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.5

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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