chr2-72972490-C-A

Variant names:

• chr2-72972490-C-A
• rs11898850
• NM_144579.3:c.626-805G>T

Variant summary

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

The NM_001330400.2(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_001330400.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330400.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFXN5	NM_144579.3	MANE Select	c.626-805G>T		intron	N/A	NP_653180.1
	SFXN5	NM_001330400.2		c.626-805G>T		intron	N/A	NP_001317329.1
	SFXN5	NM_001371737.1		c.620-805G>T		intron	N/A	NP_001358666.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFXN5	ENST00000272433.7	TSL:1 MANE Select	c.626-805G>T		intron	N/A	ENSP00000272433.2
	SFXN5	ENST00000410065.5	TSL:1	c.626-11242G>T		intron	N/A	ENSP00000387076.1
	SFXN5	ENST00000461352.5	TSL:1	n.429-3957G>T		intron	N/A

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

African (AFR) AF: 0.565 AC: 23435 AN: 41500

American (AMR) AF: 0.347 AC: 5307 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2286 AN: 5152

South Asian (SAS) AF: 0.467 AC: 2254 AN: 4828

European-Finnish (FIN) AF: 0.392 AC: 4160 AN: 10602

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29714 AN: 67972

Other (OTH) AF: 0.469 AC: 987 AN: 2106

Alfa AF: 0.449 Hom.: 50103

Bravo AF: 0.464

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.45
PhyloP100		-0.42
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs11898850; hg19: chr2-73199619;