10-119141507-C-CTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_213649.2(SFXN4):c.937-189_937-188insAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.021 (139 hom., cov: 19)
• Consequence: SFXN4 NM_213649.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.953

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-119141507-C-CTT is Benign according to our data. Variant chr10-119141507-C-CTT is described in ClinVar as [Benign]. Clinvar id is 1256640.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFXN4	NM_213649.2	c.937-189_937-188insAA		intron_variant		ENST00000355697.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFXN4	ENST00000355697.7	c.937-189_937-188insAA		intron_variant		1	NM_213649.2	P1
SFXN4	ENST00000461438.5	n.966-189_966-188insAA		intron_variant, non_coding_transcript_variant		5
SFXN4	ENST00000484960.5	n.149-189_149-188insAA		intron_variant, non_coding_transcript_variant		3
SFXN4	ENST00000490417.6	n.400-189_400-188insAA		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 2393 AN: 113306 Hom.: 139 Cov.: 19

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.00519

Gnomad AMR AF: 0.00975

Gnomad ASJ AF: 0.00367

Gnomad EAS AF: 0.00180

Gnomad SAS AF: 0.00792

Gnomad FIN AF: 0.000568

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00361

Gnomad OTH AF: 0.0184

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

GnomAD4 genome AF: 0.0211 AC: 2396 AN: 113312 Hom.: 139 Cov.: 19 AF XY: 0.0212 AC XY: 1134 AN XY: 53520

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.00975

Gnomad4 ASJ AF: 0.00367

Gnomad4 EAS AF: 0.00180

Gnomad4 SAS AF: 0.00795

Gnomad4 FIN AF: 0.000568

Gnomad4 NFE AF: 0.00361

Gnomad4 OTH AF: 0.0183

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 12, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1234472904; hg19: chr10-120901019;