10-102726547-G-C

Position:

• chr10-102726547-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178858.6(SFXN2):​c.-25-65G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 1,533,838 control chromosomes in the GnomAD database, including 452,416 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 0.74 (41686 hom., cov: 32)
  • Exomes 𝑓: 0.77 (410730 hom.)
• Consequence: SFXN2 NM_178858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

Genes affected

SFXN2 (HGNC:16086): (sideroflexin 2) Predicted to enable serine transmembrane transporter activity. Involved in mitochondrial transmembrane transport. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

SFXN2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFXN2	NM_178858.6	c.-25-65G>C		intron_variant		ENST00000369893.10	NP_849189.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFXN2	ENST00000369893.10	c.-25-65G>C		intron_variant		1	NM_178858.6	ENSP00000358909.4

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112035 AN: 152004 Hom.: 41666 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.712

GnomAD4 exome AF: 0.770 AC: 1063689 AN: 1381714 Hom.: 410730 Cov.: 21 AF XY: 0.771 AC XY: 527076 AN XY: 683464

Gnomad4 AFR exome AF: 0.628

Gnomad4 AMR exome AF: 0.812

Gnomad4 ASJ exome AF: 0.623

Gnomad4 EAS exome AF: 0.725

Gnomad4 SAS exome AF: 0.820

Gnomad4 FIN exome AF: 0.847

Gnomad4 NFE exome AF: 0.772

Gnomad4 OTH exome AF: 0.751

GnomAD4 genome AF: 0.737 AC: 112102 AN: 152124 Hom.: 41686 Cov.: 32 AF XY: 0.740 AC XY: 55055 AN XY: 74358

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.714

Alfa AF: 0.763 Hom.: 5549

Bravo AF: 0.724

Asia WGS AF: 0.755 AC: 2623 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	1.9
DANN	Benign	0.67

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

LitVar

Other links and lift over

dbSNP: rs2244647; hg19: chr10-104486304;