dbSNP rs925197: SFXN1:c.596+15C>T (chr5-175512211-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022754.7(SFXN1):c.596+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,606,772 control chromosomes in the GnomAD database, including 26,038 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.22 ( 4674 hom., cov: 33)

Exomes 𝑓: 0.16 ( 21364 hom. )

Consequence

SFXN1
NM_022754.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219

Publications

13 publications found

Variant links:

Genes affected

SFXN1 (HGNC:16085): (sideroflexin 1) Enables D-serine transmembrane transporter activity and L-serine transmembrane transporter activity. Involved in D-serine transport; L-serine transport; and serine import into mitochondrion. Located in mitochondrion. Is integral component of mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

SFXN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFXN1	NM_022754.7 link	c.596+15C>T		intron_variant	Intron 6 of 10	ENST00000321442.10	NP_073591.2	Q9H9B4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFXN1	ENST00000321442.10 link	c.596+15C>T		intron_variant	Intron 6 of 10	1	NM_022754.7	ENSP00000316905.5		Q9H9B4

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33582

AN:

152016

Hom.:

4670

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.210

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.206

GnomAD2 exomes

AF:

0.194

AC:

48690

AN:

250650

AF XY:

0.196

show subpopulations

Gnomad AFR exome

AF:

0.391

Gnomad AMR exome

AF:

0.178

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.229

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.176

GnomAD4 exome

AF:

0.158

AC:

229202

AN:

1454638

Hom.:

21364

Cov.:

AF XY:

0.162

AC XY:

117209

AN XY:

724202

show subpopulations

African (AFR)

AF:

0.390

AC:

13007

AN:

33336

American (AMR)

AF:

0.176

AC:

7871

AN:

44630

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

5146

AN:

26076

East Asian (EAS)

AF:

0.233

AC:

9238

AN:

39654

South Asian (SAS)

AF:

0.332

AC:

28531

AN:

85966

European-Finnish (FIN)

AF:

0.139

AC:

7406

AN:

53276

Middle Eastern (MID)

AF:

0.226

AC:

1301

AN:

5754

European-Non Finnish (NFE)

AF:

0.132

AC:

146292

AN:

1105780

Other (OTH)

AF:

0.173

AC:

10410

AN:

60166

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

8828

17656

26485

35313

44141

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5634

11268

16902

22536

28170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.221

AC:

33619

AN:

152134

Hom.:

4674

Cov.:

AF XY:

0.221

AC XY:

16440

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.389

AC:

16129

AN:

41456

American (AMR)

AF:

0.165

AC:

2528

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

688

AN:

3470

East Asian (EAS)

AF:

0.222

AC:

1152

AN:

5180

South Asian (SAS)

AF:

0.351

AC:

1691

AN:

4824

European-Finnish (FIN)

AF:

0.138

AC:

1461

AN:

10582

Middle Eastern (MID)

AF:

0.219

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.137

AC:

9343

AN:

68014

Other (OTH)

AF:

0.207

AC:

438

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1243

2487

3730

4974

6217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.188

Hom.:

1055

Bravo

AF:

0.228

Asia WGS

AF:

0.314

AC:

1093

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

1.9

(source)

DANN

Benign

0.75

PhyloP100

0.22

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over