rs10514828

Variant names:

• chr9-37885459-C-T
• rs10514828
• ENST00000496760.5:n.409-3828G>A

Variant summary

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

The ENST00000496760.5(SLC25A51):​n.409-3828G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 150,980 control chromosomes in the GnomAD database, including 565 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 0.054 (565 hom., cov: 31)
• Consequence: SLC25A51 ENST00000496760.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 2 publications found

Genes affected

SLC25A51 (HGNC:23323): (solute carrier family 25 member 51) Enables NAD transmembrane transporter activity. Involved in mitochondrial NAD transmembrane transport. Located in mitochondrion. Is active in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255872 (HGNC:):

PAICSP1 (HGNC:8588): (phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 1)

TMX2P1 (HGNC:49916): (thioredoxin related transmembrane protein 2 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAICSP1		n.37885459C>T		intragenic_variant
SLC25A51	NR_024872.3	n.210-3828G>A		intron_variant	Intron 3 of 4
SLC25A51	NR_024873.3	n.183-3828G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A51	ENST00000496760.5	n.409-3828G>A		intron_variant	Intron 2 of 3	1
ENSG00000255872	ENST00000540557.1	n.*681+14370G>A		intron_variant	Intron 7 of 11	5		ENSP00000457548.1
TMX2P1	ENST00000436507.2	n.-224C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8132 AN: 150880 Hom.: 562 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.0246

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.00354

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0540 AC: 8147 AN: 150980 Hom.: 565 Cov.: 31 AF XY: 0.0531 AC XY: 3910 AN XY: 73628

African (AFR) AF: 0.156 AC: 6423 AN: 41070

American (AMR) AF: 0.0443 AC: 672 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3468

East Asian (EAS) AF: 0.0786 AC: 401 AN: 5104

South Asian (SAS) AF: 0.0240 AC: 115 AN: 4792

European-Finnish (FIN) AF: 0.0161 AC: 165 AN: 10232

Middle Eastern (MID) AF: 0.0276 AC: 8 AN: 290

European-Non Finnish (NFE) AF: 0.00355 AC: 241 AN: 67870

Other (OTH) AF: 0.0421 AC: 88 AN: 2088

Alfa AF: 0.0313 Hom.: 31

Bravo AF: 0.0617

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.60
DANN	Benign	0.57
PhyloP100		-2.9
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: rs10514828; hg19: chr9-37885456;