10-101037108-AG-AGG

Variant names:

• chr10-101037108-A-AG
• rs563028036
• NM_030971.6:c.628dupG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_030971.6(SFXN3):​c.628dupG​(p.Ala210GlyfsTer98) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SFXN3 NM_030971.6 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFXN3	NM_030971.6	MANE Select	c.628dupG	p.Ala210GlyfsTer98	frameshift	Exon 8 of 12	NP_112233.3
	SFXN3	NM_001388027.1		c.652dupG	p.Ala218GlyfsTer98	frameshift	Exon 8 of 12	NP_001374956.1	B4DRS6
	SFXN3	NM_001388028.1		c.652dupG	p.Ala218GlyfsTer98	frameshift	Exon 8 of 12	NP_001374957.1	B4DRS6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFXN3	ENST00000393459.6	TSL:5 MANE Select	c.628dupG	p.Ala210GlyfsTer98	frameshift	Exon 8 of 12	ENSP00000377103.1	Q9BWM7
	SFXN3	ENST00000698791.1		c.640dupG	p.Ala214GlyfsTer98	frameshift	Exon 7 of 11	ENSP00000513933.1	A0A8V8TP06
	SFXN3	ENST00000896239.1		c.628dupG	p.Ala210GlyfsTer98	frameshift	Exon 8 of 12	ENSP00000566298.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs563028036; hg19: chr10-102796865;