Genetic Variant NM_030971.6:c.771+71C>T (chr10-101037502-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_030971.6(SFXN3):c.771+71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,613,064 control chromosomes in the GnomAD database, including 58,954 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 0.20 ( 3835 hom., cov: 32)

Exomes 𝑓: 0.27 ( 55119 hom. )

Consequence

SFXN3
NM_030971.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Publications

7 publications found

Variant links:

Genes affected

SFXN3 (HGNC:16087): (sideroflexin 3) Enables serine transmembrane transporter activity. Involved in serine import into mitochondrion. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

SFXN3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030971.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SFXN3	NM_030971.6	MANE Select	c.771+71C>T	intron	N/A	NP_112233.3
SFXN3	NM_001388027.1		c.795+71C>T	intron	N/A	NP_001374956.1
SFXN3	NM_001388028.1		c.795+71C>T	intron	N/A	NP_001374957.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SFXN3	ENST00000393459.6	TSL:5 MANE Select	c.771+71C>T	intron	N/A	ENSP00000377103.1
SFXN3	ENST00000698791.1		c.783+71C>T	intron	N/A	ENSP00000513933.1
SFXN3	ENST00000896239.1		c.771+71C>T	intron	N/A	ENSP00000566298.1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30228

AN:

152058

Hom.:

3836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0491

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.217

GnomAD4 exome

AF:

0.269

AC:

392788

AN:

1460888

Hom.:

55119

Cov.:

AF XY:

0.270

AC XY:

196004

AN XY:

726740

show subpopulations

African (AFR)

AF:

0.0401

AC:

1343

AN:

33470

American (AMR)

AF:

0.131

AC:

5863

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.366

AC:

9545

AN:

26114

East Asian (EAS)

AF:

0.130

AC:

5175

AN:

39698

South Asian (SAS)

AF:

0.249

AC:

21443

AN:

86212

European-Finnish (FIN)

AF:

0.212

AC:

11286

AN:

53244

Middle Eastern (MID)

AF:

0.241

AC:

1320

AN:

5476

European-Non Finnish (NFE)

AF:

0.289

AC:

321041

AN:

1111658

Other (OTH)

AF:

0.261

AC:

15772

AN:

60318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

17056

34111

51167

68222

85278

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10532

21064

31596

42128

52660

<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:

0.199

AC:

30215

AN:

152176

Hom.:

3835

Cov.:

AF XY:

0.195

AC XY:

14536

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.0489

AC:

2033

AN:

41544

American (AMR)

AF:

0.177

AC:

2710

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1209

AN:

3472

East Asian (EAS)

AF:

0.167

AC:

866

AN:

5178

South Asian (SAS)

AF:

0.248

AC:

1193

AN:

4820

European-Finnish (FIN)

AF:

0.210

AC:

2224

AN:

10586

Middle Eastern (MID)

AF:

0.271

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.282

AC:

19177

AN:

67960

Other (OTH)

AF:

0.215

AC:

454

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1156

2312

3469

4625

5781

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<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:

0.243

Hom.:

2051

Bravo

AF:

0.188

Asia WGS

AF:

0.181

AC:

628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

(source)

DANN

Benign

0.46

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.22

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.22

Position offset: 6

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over