dbSNP rs1234472904: SFXN4:c.937-195_937-189delAAAAAAA (chr10-119141507-CTTTTTTT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_213649.2(SFXN4):c.937-195_937-189delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 19)

Consequence

SFXN4
NM_213649.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.54

Variant links:

Genes affected

SFXN4 (HGNC:16088): (sideroflexin 4) This gene encodes a member of the sideroflexin family. The encoded protein is a transmembrane protein of the inner mitochondrial membrane, and is required for mitochondrial respiratory homeostasis and erythropoiesis. Mutations in this gene are associated with mitochondriopathy and macrocytic anemia. Alternatively spliced transcript variants have been found in this gene. [provided by RefSeq, Jan 2014]

SFXN4 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFXN4	NM_213649.2 link	c.937-195_937-189delAAAAAAA		intron_variant	Intron 13 of 13	ENST00000355697.7	NP_998814.1	Q6P4A7-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SFXN4	ENST00000355697.7 link	c.937-195_937-189delAAAAAAA	intron_variant	Intron 13 of 13	1	NM_213649.2	ENSP00000347924.2	Q6P4A7-1
SFXN4	ENST00000461438.5 link	n.966-195_966-189delAAAAAAA	intron_variant	Intron 14 of 14	5
SFXN4	ENST00000484960.5 link	n.149-195_149-189delAAAAAAA	intron_variant	Intron 2 of 2	3
SFXN4	ENST00000490417.6 link	n.400-195_400-189delAAAAAAA	intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.