rs10491682

Positions:

• chr9-37895175-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A51	NM_033412.4	c.-43+4654A>G		intron_variant		ENST00000242275.7
SLC25A51	NR_024872.3	n.209+4654A>G		intron_variant, non_coding_transcript_variant
SLC25A51	NR_024873.3	n.182+4654A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A51	ENST00000242275.7	c.-43+4654A>G		intron_variant		2	NM_033412.4	P1
SLC25A51	ENST00000496760.5	n.408+4654A>G		intron_variant, non_coding_transcript_variant		1
SLC25A51	ENST00000377716.6	c.-43+4654A>G		intron_variant		3		P1

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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0516

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.00370

Gnomad4 OTH AF: 0.0539

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491682; hg19: chr9-37895172;