10-119141507-C-CT

Variant names:

• chr10-119141507-C-CT
• rs1234472904
• NM_213649.2:c.937-189dupA

Variant summary

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

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

• Frequency: Genomes: 𝑓 0.17 (2267 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-CT is Benign according to our data. Variant chr10-119141507-C-CT is described in ClinVar as [Benign]. Clinvar id is 1224878.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFXN4	ENST00000355697.7	c.937-189_937-188insA		intron_variant	Intron 13 of 13	1	NM_213649.2	ENSP00000347924.2
SFXN4	ENST00000461438.5	n.966-189_966-188insA		intron_variant	Intron 14 of 14	5
SFXN4	ENST00000484960.5	n.149-189_149-188insA		intron_variant	Intron 2 of 2	3
SFXN4	ENST00000490417.6	n.400-189_400-188insA		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 19689 AN: 113336 Hom.: 2271 Cov.: 19

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.174 AC: 19680 AN: 113342 Hom.: 2267 Cov.: 19 AF XY: 0.167 AC XY: 8966 AN XY: 53550

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.186

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 10, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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;