chr10-119141464-ATT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_213649.2(SFXN4):​c.937-147_937-146del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 178,794 control chromosomes in the GnomAD database, including 57,500 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.72 ( 39588 hom., cov: 0)
Exomes 𝑓: 0.81 ( 57500 hom. )
Failed GnomAD Quality Control

Consequence

SFXN4
NM_213649.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0850
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 10-119141464-ATT-A is Benign according to our data. Variant chr10-119141464-ATT-A is described in ClinVar as [Benign]. Clinvar id is 1225080.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SFXN4NM_213649.2 linkuse as main transcriptc.937-147_937-146del intron_variant ENST00000355697.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SFXN4ENST00000355697.7 linkuse as main transcriptc.937-147_937-146del intron_variant 1 NM_213649.2 P1Q6P4A7-1
SFXN4ENST00000461438.5 linkuse as main transcriptn.966-147_966-146del intron_variant, non_coding_transcript_variant 5
SFXN4ENST00000484960.5 linkuse as main transcriptn.149-147_149-146del intron_variant, non_coding_transcript_variant 3
SFXN4ENST00000490417.6 linkuse as main transcriptn.400-147_400-146del intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.724
AC:
105103
AN:
145120
Hom.:
39568
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.491
Gnomad AMI
AF:
0.868
Gnomad AMR
AF:
0.743
Gnomad ASJ
AF:
0.761
Gnomad EAS
AF:
0.761
Gnomad SAS
AF:
0.721
Gnomad FIN
AF:
0.868
Gnomad MID
AF:
0.675
Gnomad NFE
AF:
0.830
Gnomad OTH
AF:
0.718
GnomAD4 exome
AF:
0.808
AC:
144546
AN:
178794
Hom.:
57500
AF XY:
0.808
AC XY:
77508
AN XY:
95922
show subpopulations
Gnomad4 AFR exome
AF:
0.509
Gnomad4 AMR exome
AF:
0.767
Gnomad4 ASJ exome
AF:
0.763
Gnomad4 EAS exome
AF:
0.755
Gnomad4 SAS exome
AF:
0.746
Gnomad4 FIN exome
AF:
0.851
Gnomad4 NFE exome
AF:
0.832
Gnomad4 OTH exome
AF:
0.795
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.724
AC:
105158
AN:
145212
Hom.:
39588
Cov.:
0
AF XY:
0.724
AC XY:
50862
AN XY:
70228
show subpopulations
Gnomad4 AFR
AF:
0.491
Gnomad4 AMR
AF:
0.743
Gnomad4 ASJ
AF:
0.761
Gnomad4 EAS
AF:
0.761
Gnomad4 SAS
AF:
0.721
Gnomad4 FIN
AF:
0.868
Gnomad4 NFE
AF:
0.830
Gnomad4 OTH
AF:
0.721

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 submitterclinical testingGeneDxAug 06, 2019- -

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.

Other links and lift over

dbSNP: rs34287145; hg19: chr10-120900976; API