NM_178858.6:c.-25-65G>C

Variant names:

• chr10-102726547-G-C
• rs2244647
• NM_178858.6:c.-25-65G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SFXN2	NM_178858.6	c.-25-65G>C		intron_variant	Intron 1 of 11	ENST00000369893.10	NP_849189.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFXN2	ENST00000369893.10	c.-25-65G>C		intron_variant	Intron 1 of 11	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

African (AFR) AF: 0.628 AC: 19984 AN: 31802

American (AMR) AF: 0.812 AC: 33108 AN: 40774

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 13939 AN: 22372

East Asian (EAS) AF: 0.725 AC: 28366 AN: 39112

South Asian (SAS) AF: 0.820 AC: 62838 AN: 76608

European-Finnish (FIN) AF: 0.847 AC: 39460 AN: 46614

Middle Eastern (MID) AF: 0.707 AC: 3655 AN: 5168

European-Non Finnish (NFE) AF: 0.772 AC: 819261 AN: 1061904

Other (OTH) AF: 0.751 AC: 43078 AN: 57360

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

African (AFR) AF: 0.645 AC: 26743 AN: 41494

American (AMR) AF: 0.752 AC: 11484 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3747 AN: 5150

South Asian (SAS) AF: 0.819 AC: 3957 AN: 4830

European-Finnish (FIN) AF: 0.851 AC: 9024 AN: 10604

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52691 AN: 67984

Other (OTH) AF: 0.714 AC: 1507 AN: 2112

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
PhyloP100		0.43
PromoterAI		-0.048	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2244647; hg19: chr10-104486304;