rs2421099

Variant names:

• chr2-73068935-T-A
• rs2421099
• NM_144579.3:c.102+2669A>T

Your query was ambiguous. Multiple possible variants found:

• chr2-73068935-T-A
• chr2-73068935-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144579.3(SFXN5):​c.102+2669A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 149,182 control chromosomes in the GnomAD database, including 1,861 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 0.15 (1861 hom., cov: 30)
• Consequence: SFXN5 NM_144579.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144579.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFXN5	NM_144579.3	MANE Select	c.102+2669A>T		intron	N/A	NP_653180.1	Q8TD22
	SFXN5	NM_001330400.2		c.102+2669A>T		intron	N/A	NP_001317329.1
	SFXN5	NM_001371737.1		c.41+2669A>T		intron	N/A	NP_001358666.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFXN5	ENST00000272433.7	TSL:1 MANE Select	c.102+2669A>T		intron	N/A	ENSP00000272433.2	Q8TD22
	SFXN5	ENST00000410065.5	TSL:1	c.102+2669A>T		intron	N/A	ENSP00000387076.1	B8ZZJ6
	SFXN5	ENST00000868596.1		c.102+2669A>T		intron	N/A	ENSP00000538655.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21680 AN: 149062 Hom.: 1865 Cov.: 30

Gnomad AFR AF: 0.0890

Gnomad AMI AF: 0.0661

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.145 AC: 21686 AN: 149182 Hom.: 1861 Cov.: 30 AF XY: 0.153 AC XY: 11089 AN XY: 72644

African (AFR) AF: 0.0889 AC: 3583 AN: 40300

American (AMR) AF: 0.179 AC: 2689 AN: 15002

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 403 AN: 3432

East Asian (EAS) AF: 0.414 AC: 2083 AN: 5034

South Asian (SAS) AF: 0.186 AC: 871 AN: 4680

European-Finnish (FIN) AF: 0.235 AC: 2393 AN: 10164

Middle Eastern (MID) AF: 0.0793 AC: 23 AN: 290

European-Non Finnish (NFE) AF: 0.138 AC: 9276 AN: 67286

Other (OTH) AF: 0.146 AC: 305 AN: 2086

Alfa AF: 0.126 Hom.: 176

Bravo AF: 0.140

Asia WGS AF: 0.273 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.3
DANN	Benign	0.91
PhyloP100		-0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2421099; hg19: chr2-73296064;