chr10-119141507-C-CTTT

Variant names:

• chr10-119141507-C-CTTT
• rs1234472904
• NM_213649.2:c.937-191_937-189dupAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_213649.2(SFXN4):​c.937-191_937-189dupAAA 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: 𝑓 0.00096 (3 hom., cov: 19)
• Consequence: SFXN4 NM_213649.2 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000962 (109/113346) while in subpopulation AFR AF= 0.00215 (60/27920). AF 95% confidence interval is 0.00171. There are 3 homozygotes in gnomad4. There are 53 alleles in male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFXN4	NM_213649.2	c.937-191_937-189dupAAA		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_937-188insAAA		intron_variant	Intron 13 of 13	1	NM_213649.2	ENSP00000347924.2
SFXN4	ENST00000461438.5	n.966-189_966-188insAAA		intron_variant	Intron 14 of 14	5
SFXN4	ENST00000484960.5	n.149-189_149-188insAAA		intron_variant	Intron 2 of 2	3
SFXN4	ENST00000490417.6	n.400-189_400-188insAAA		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.000962 AC: 109 AN: 113340 Hom.: 3 Cov.: 19

Gnomad AFR AF: 0.00215

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000289

Gnomad ASJ AF: 0.000666

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.000293

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000648

Gnomad OTH AF: 0.00205

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

GnomAD4 genome AF: 0.000962 AC: 109 AN: 113346 Hom.: 3 Cov.: 19 AF XY: 0.000990 AC XY: 53 AN XY: 53538

Gnomad4 AFR AF: 0.00215

Gnomad4 AMR AF: 0.000289

Gnomad4 ASJ AF: 0.000666

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.000294

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000648

Gnomad4 OTH AF: 0.00203

ClinVar

Not reported in ClinVar

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;