rs1219999

Variant names:

• chr1-108174381-C-T
• rs1069903
• NM_013386.5:c.398+7560G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-108174381-C-T
• chrNW_017852928.1-186557-T-C

Variant summary

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

The NM_013386.5(SLC25A24):​c.398+7560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,092 control chromosomes in the GnomAD database, including 38,368 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 0.71 (38368 hom., cov: 32)
• Consequence: SLC25A24 NM_013386.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 2 publications found

Genes affected

SLC25A24 (HGNC:20662): (solute carrier family 25 member 24) This gene encodes a carrier protein that transports ATP-Mg exchanging it for phosphate. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

SLC25A24 Gene-Disease associations (from GenCC):

• Fontaine progeroid syndrome

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, PanelApp Australia, Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013386.5. 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
	SLC25A24	NM_013386.5	MANE Select	c.398+7560G>A		intron	N/A	NP_037518.3
	SLC25A24	NM_213651.3		c.341+7560G>A		intron	N/A	NP_998816.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A24	ENST00000565488.6	TSL:1 MANE Select	c.398+7560G>A		intron	N/A	ENSP00000457733.1
	SLC25A24	ENST00000370041.4	TSL:1	c.341+7560G>A		intron	N/A	ENSP00000359058.4
	SLC25A24	ENST00000264128.13	TSL:5	n.310+11447G>A		intron	N/A	ENSP00000264128.9

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107346 AN: 151974 Hom.: 38347 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.706 AC: 107412 AN: 152092 Hom.: 38368 Cov.: 32 AF XY: 0.699 AC XY: 51963 AN XY: 74328

African (AFR) AF: 0.810 AC: 33633 AN: 41508

American (AMR) AF: 0.640 AC: 9782 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2558 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3366 AN: 5134

South Asian (SAS) AF: 0.558 AC: 2690 AN: 4820

European-Finnish (FIN) AF: 0.632 AC: 6683 AN: 10570

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46213 AN: 67986

Other (OTH) AF: 0.729 AC: 1542 AN: 2114

Alfa AF: 0.688 Hom.: 4706

Bravo AF: 0.716

Asia WGS AF: 0.606 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.79
DANN	Benign	0.17
PhyloP100		-0.63
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: rs1069903; hg19: chr1-108717003;