rs10819354

Variant names:

• chr9-128091211-A-G
• rs10819354
• NM_001330988.2:c.262-9885A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-128091211-A-G
• chr9-128091211-A-T

Variant summary

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

The NM_001330988.2(SLC25A25):​c.262-9885A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 155,312 control chromosomes in the GnomAD database, including 44,962 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 0.74 (43802 hom., cov: 31)
  • Exomes 𝑓: 0.84 (1160 hom.)
• Consequence: SLC25A25 NM_001330988.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 5 publications found

Genes affected

SLC25A25 (HGNC:20663): (solute carrier family 25 member 25) The protein encoded by this gene belongs to the family of calcium-binding mitochondrial carriers, with a characteristic mitochondrial carrier domain at the C-terminus. These proteins are found in the inner membranes of mitochondria, and function as transport proteins. They shuttle metabolites, nucleotides and cofactors through the mitochondrial membrane and thereby connect and/or regulate cytoplasm and matrix functions. This protein may function as an ATP-Mg/Pi carrier that mediates the transport of Mg-ATP in exchange for phosphate, and likely responsible for the net uptake or efflux of adenine nucleotides into or from the mitochondria. Alternatively spliced transcript variants encoding different isoforms with a common C-terminus but variable N-termini have been described for this gene. [provided by RefSeq, Jul 2012]

ENSG00000230536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330988.2. 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
	SLC25A25	NM_001330988.2	MANE Select	c.262-9885A>G		intron	N/A	NP_001317917.1
	SLC25A25	NM_001006641.4		c.262-9885A>G		intron	N/A	NP_001006642.1
	SLC25A25	NM_001265614.3		c.-660A>G		upstream_gene	N/A	NP_001252543.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A25	ENST00000373069.10	TSL:5 MANE Select	c.262-9885A>G		intron	N/A	ENSP00000362160.5
	SLC25A25	ENST00000373068.6	TSL:1	c.262-9885A>G		intron	N/A	ENSP00000362159.2
	ENSG00000230536	ENST00000453870.1	TSL:3	n.523T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112968 AN: 151956 Hom.: 43794 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.757

GnomAD4 exome AF: 0.843 AC: 2730 AN: 3238 Hom.: 1160 Cov.: 3 AF XY: 0.860 AC XY: 1348 AN XY: 1568

African (AFR) AF: 0.419 AC: 31 AN: 74

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 16 AN: 20

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.742 AC: 46 AN: 62

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.856 AC: 2534 AN: 2962

Other (OTH) AF: 0.852 AC: 92 AN: 108

GnomAD4 genome AF: 0.743 AC: 113000 AN: 152074 Hom.: 43802 Cov.: 31 AF XY: 0.744 AC XY: 55303 AN XY: 74348

African (AFR) AF: 0.502 AC: 20793 AN: 41422

American (AMR) AF: 0.768 AC: 11738 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2943 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4199 AN: 5176

South Asian (SAS) AF: 0.736 AC: 3540 AN: 4810

European-Finnish (FIN) AF: 0.882 AC: 9351 AN: 10604

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57874 AN: 67986

Other (OTH) AF: 0.754 AC: 1590 AN: 2110

Alfa AF: 0.773 Hom.: 7112

Bravo AF: 0.725

Asia WGS AF: 0.738 AC: 2571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.57
PhyloP100		-0.097
PromoterAI		-0.0056	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10819354; hg19: chr9-130853490; COSMIC: COSV107480598; COSMIC: COSV107480598;