chr9-37885459-C-T

Position:

• chr9-37885459-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000496760.5(SLC25A51):​n.409-3828G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91

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=-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/exons	MANE	UniProt
SLC25A51	NR_024872.3	n.210-3828G>A		intron_variant, non_coding_transcript_variant
SLC25A51	NR_024873.3	n.183-3828G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A51	ENST00000496760.5	n.409-3828G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0443

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0786

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.00355

Gnomad4 OTH AF: 0.0421

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10514828; hg19: chr9-37885456;