Variant rs2275382 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFXN3	NM_030971.6 linkuse as main transcript	c.771+71C>T		intron_variant		ENST00000393459.6	NP_112233.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFXN3	ENST00000393459.6 linkuse as main transcript	c.771+71C>T		intron_variant		5	NM_030971.6	ENSP00000377103	P1

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

Gnomad4 AFR exome

AF:

0.0401

Gnomad4 AMR exome

AF:

0.131

Gnomad4 ASJ exome

AF:

0.366

Gnomad4 EAS exome

AF:

0.130

Gnomad4 SAS exome

AF:

0.249

Gnomad4 FIN exome

AF:

0.212

Gnomad4 NFE exome

AF:

0.289

Gnomad4 OTH exome

AF:

0.261

GnomAD4 genome

AF:

0.199

AC:

30215

AN:

152176

Hom.:

3835

Cov.:

AF XY:

0.195

AC XY:

14536

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0489

Gnomad4 AMR

AF:

0.177

Gnomad4 ASJ

AF:

0.348

Gnomad4 EAS

AF:

0.167

Gnomad4 SAS

AF:

0.248

Gnomad4 FIN

AF:

0.210

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.248

Hom.:

1256

Bravo

AF:

0.188

Asia WGS

AF:

0.181

AC:

628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

DANN

Benign

0.46

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over