dbSNP rs6897931: SFXN1:c.872+50C>A (chr5-175522472-C-A) – 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.872+50C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 1,563,470 control chromosomes in the GnomAD database, including 1,148 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 0.046 ( 269 hom., cov: 32)

Exomes 𝑓: 0.018 ( 879 hom. )

Consequence

SFXN1
NM_022754.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.952

Publications

2 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:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFXN1	NM_022754.7 link	c.872+50C>A		intron_variant	Intron 10 of 10	ENST00000321442.10	NP_073591.2	Q9H9B4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SFXN1	ENST00000321442.10 link	c.872+50C>A	intron_variant	Intron 10 of 10	1	NM_022754.7	ENSP00000316905.5	Q9H9B4
SFXN1	ENST00000507823.5 link	n.*722C>A	non_coding_transcript_exon_variant	Exon 10 of 10	2		ENSP00000421982.1	D6RAE9
SFXN1	ENST00000507823.5 link	n.*722C>A	3_prime_UTR_variant	Exon 10 of 10	2		ENSP00000421982.1	D6RAE9
SFXN1	ENST00000421887.2 link	n.131+50C>A	intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.0459

AC:

6964

AN:

151784

Hom.:

268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0980

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0971

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.0227

Gnomad SAS

AF:

0.0748

Gnomad FIN

AF:

0.0175

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00915

Gnomad OTH

AF:

0.0465

GnomAD2 exomes

AF:

0.0406

AC:

9301

AN:

229368

AF XY:

0.0379

show subpopulations

Gnomad AFR exome

AF:

0.103

Gnomad AMR exome

AF:

0.128

Gnomad ASJ exome

AF:

0.0197

Gnomad EAS exome

AF:

0.0216

Gnomad FIN exome

AF:

0.0186

Gnomad NFE exome

AF:

0.00973

Gnomad OTH exome

AF:

0.0263

GnomAD4 exome

AF:

0.0182

AC:

25636

AN:

1411568

Hom.:

879

Cov.:

AF XY:

0.0192

AC XY:

13546

AN XY:

704204

show subpopulations

African (AFR)

AF:

0.103

AC:

3265

AN:

31698

American (AMR)

AF:

0.121

AC:

4627

AN:

38260

Ashkenazi Jewish (ASJ)

AF:

0.0188

AC:

472

AN:

25044

East Asian (EAS)

AF:

0.0173

AC:

677

AN:

39244

South Asian (SAS)

AF:

0.0746

AC:

6072

AN:

81346

European-Finnish (FIN)

AF:

0.0167

AC:

856

AN:

51128

Middle Eastern (MID)

AF:

0.0406

AC:

228

AN:

5614

European-Non Finnish (NFE)

AF:

0.00737

AC:

7964

AN:

1080654

Other (OTH)

AF:

0.0252

AC:

1475

AN:

58580

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1155

2311

3466

4622

5777

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.0459

AC:

6978

AN:

151902

Hom.:

269

Cov.:

AF XY:

0.0478

AC XY:

3547

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.0979

AC:

4055

AN:

41416

American (AMR)

AF:

0.0974

AC:

1486

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

AN:

3464

East Asian (EAS)

AF:

0.0230

AC:

119

AN:

5178

South Asian (SAS)

AF:

0.0742

AC:

357

AN:

4810

European-Finnish (FIN)

AF:

0.0175

AC:

184

AN:

10486

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00915

AC:

622

AN:

67982

Other (OTH)

AF:

0.0460

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

314

628

943

1257

1571

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0237

Hom.:

159

Bravo

AF:

0.0545

Asia WGS

AF:

0.0680

AC:

234

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.59

(source)

DANN

Benign

0.46

PhyloP100

-0.95

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