NM_033412.4:c.-43+4654A>G

Variant names:

• chr9-37895175-T-C
• rs10491682
• NM_033412.4:c.-43+4654A>G

Variant summary

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

The NM_033412.4(SLC25A51):​c.-43+4654A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 152,250 control chromosomes in the GnomAD database, including 1,137 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 0.074 (1137 hom., cov: 32)
• Consequence: SLC25A51 NM_033412.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033412.4. 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
	SLC25A51	NM_033412.4	MANE Select	c.-43+4654A>G		intron	N/A	NP_219480.1
	SLC25A51	NR_024872.3		n.209+4654A>G		intron	N/A
	SLC25A51	NR_024873.3		n.182+4654A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A51	ENST00000242275.7	TSL:2 MANE Select	c.-43+4654A>G		intron	N/A	ENSP00000242275.6
	SLC25A51	ENST00000496760.5	TSL:1	n.408+4654A>G		intron	N/A
	ENSG00000255872	ENST00000540557.1	TSL:5	n.*681+4654A>G		intron	N/A	ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11192 AN: 152132 Hom.: 1130 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00369

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0737 AC: 11215 AN: 152250 Hom.: 1137 Cov.: 32 AF XY: 0.0721 AC XY: 5367 AN XY: 74464

African (AFR) AF: 0.225 AC: 9342 AN: 41502

American (AMR) AF: 0.0516 AC: 789 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.0767 AC: 398 AN: 5190

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4828

European-Finnish (FIN) AF: 0.0155 AC: 165 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00370 AC: 252 AN: 68030

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0469 Hom.: 87

Bravo AF: 0.0847

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.59
PhyloP100		-0.40
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: rs10491682; hg19: chr9-37895172;