10-119141507-CT-C

Variant summary

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

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

• Frequency: Genomes: 𝑓 0.022 (48 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-CT-C is Benign according to our data. Variant chr10-119141507-CT-C is described in ClinVar as [Benign]. Clinvar id is 1256922.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0773 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 2475 AN: 113322 Hom.: 48 Cov.: 19

Gnomad AFR AF: 0.0803

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.000666

Gnomad EAS AF: 0.00103

Gnomad SAS AF: 0.00117

Gnomad FIN AF: 0.00303

Gnomad MID AF: 0.0163

Gnomad NFE AF: 0.00128

Gnomad OTH AF: 0.0150

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

GnomAD4 genome AF: 0.0218 AC: 2471 AN: 113326 Hom.: 48 Cov.: 19 AF XY: 0.0217 AC XY: 1160 AN XY: 53524

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.0110

Gnomad4 ASJ AF: 0.000666

Gnomad4 EAS AF: 0.00103

Gnomad4 SAS AF: 0.000883

Gnomad4 FIN AF: 0.00303

Gnomad4 NFE AF: 0.00128

Gnomad4 OTH AF: 0.0149

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 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs1234472904; hg19: chr10-120901019;