Genetic Variant NM_022754.7:c.*6G>A (chr5-175526740-G-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.*6G>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 0.165 in 1,609,326 control chromosomes in the GnomAD database, including 26,664 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 0.23 ( 4970 hom., cov: 33)

Exomes 𝑓: 0.16 ( 21694 hom. )

Consequence

SFXN1
NM_022754.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.440

Publications

15 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFXN1	NM_022754.7 link	c.*6G>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000321442.10	NP_073591.2	Q9H9B4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFXN1	ENST00000321442.10 link	c.*6G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_022754.7	ENSP00000316905.5		Q9H9B4
SFXN1	ENST00000421887.2 link	n.408G>A		non_coding_transcript_exon_variant	Exon 4 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34275

AN:

152144

Hom.:

4963

Cov.:

show subpopulations

Gnomad AFR

AF:

0.408

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.168

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.203

GnomAD2 exomes

AF:

0.194

AC:

48784

AN:

251158

AF XY:

0.196

show subpopulations

Gnomad AFR exome

AF:

0.408

Gnomad AMR exome

AF:

0.179

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.231

Gnomad FIN exome

AF:

0.123

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.175

GnomAD4 exome

AF:

0.158

AC:

230441

AN:

1457064

Hom.:

21694

Cov.:

AF XY:

0.162

AC XY:

117802

AN XY:

725230

show subpopulations

African (AFR)

AF:

0.409

AC:

13643

AN:

33380

American (AMR)

AF:

0.177

AC:

7924

AN:

44682

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

5139

AN:

26078

East Asian (EAS)

AF:

0.234

AC:

9282

AN:

39680

South Asian (SAS)

AF:

0.332

AC:

28643

AN:

86148

European-Finnish (FIN)

AF:

0.120

AC:

6397

AN:

53416

Middle Eastern (MID)

AF:

0.227

AC:

1308

AN:

5756

European-Non Finnish (NFE)

AF:

0.133

AC:

147616

AN:

1107706

Other (OTH)

AF:

0.174

AC:

10489

AN:

60218

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

8720

17440

26161

34881

43601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5698

11396

17094

22792

28490

<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:

0.225

AC:

34323

AN:

152262

Hom.:

4970

Cov.:

AF XY:

0.224

AC XY:

16675

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.408

AC:

16960

AN:

41536

American (AMR)

AF:

0.168

AC:

2565

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

687

AN:

3472

East Asian (EAS)

AF:

0.223

AC:

1156

AN:

5180

South Asian (SAS)

AF:

0.354

AC:

1707

AN:

4828

European-Finnish (FIN)

AF:

0.116

AC:

1234

AN:

10610

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.138

AC:

9393

AN:

68022

Other (OTH)

AF:

0.205

AC:

433

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1291

2581

3872

5162

6453

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

346

692

1038

1384

1730

<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:

0.169

Hom.:

4197

Bravo

AF:

0.234

Asia WGS

AF:

0.327

AC:

1136

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.1

(source)

DANN

Benign

0.51

PhyloP100

0.44

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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