rs11898850

chr2-72972490-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144579.3(SFXN5):c.626-805G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,122 control chromosomes in the GnomAD database, including 16,864 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (16864 hom., cov: 33)
• Consequence: SFXN5 NM_144579.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

Genes affected

SFXN5 (HGNC:16073): (sideroflexin 5) Predicted to enable citrate transmembrane transporter activity. Predicted to be involved in citrate transport and mitochondrial transmembrane transport. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFXN5	NM_144579.3	c.626-805G>T		intron_variant		ENST00000272433.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFXN5	ENST00000272433.7	c.626-805G>T		intron_variant		1	NM_144579.3	P1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70629 AN: 152004 Hom.: 16853 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.465 AC: 70667 AN: 152122 Hom.: 16864 Cov.: 33 AF XY: 0.460 AC XY: 34225 AN XY: 74368

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.469

Alfa AF: 0.443 Hom.: 20765

Bravo AF: 0.464

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.41
Dann	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11898850; hg19: chr2-73199619;