rs150888153

Positions:

• chr3-140963071-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001104647.3(SLC25A36):​c.285-56T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 1,094,584 control chromosomes in the GnomAD database, including 216 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 0.014 (21 hom., cov: 32)
  • Exomes 𝑓: 0.019 (195 hom.)
• Consequence: SLC25A36 NM_001104647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679

Genes affected

SLC25A36 (HGNC:25554): (solute carrier family 25 member 36) Enables pyrimidine nucleotide transmembrane transporter activity. Involved in mitochondrial genome maintenance; pyrimidine nucleotide transport; and regulation of mitochondrial membrane potential. Located in mitochondrion. [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=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0137 (2081/152114) while in subpopulation NFE AF= 0.0218 (1478/67878). AF 95% confidence interval is 0.0209. There are 21 homozygotes in gnomad4. There are 995 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 21 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A36	NM_001104647.3	c.285-56T>A		intron_variant		ENST00000324194.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A36	ENST00000324194.12	c.285-56T>A		intron_variant		1	NM_001104647.3	P3

Frequencies

GnomAD3 genomes AF: 0.0137 AC: 2083 AN: 151996 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.00343

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0163

GnomAD4 exome AF: 0.0187 AC: 17664 AN: 942470 Hom.: 195 AF XY: 0.0184 AC XY: 8879 AN XY: 482586

Gnomad4 AFR exome AF: 0.00318

Gnomad4 AMR exome AF: 0.0110

Gnomad4 ASJ exome AF: 0.0152

Gnomad4 EAS exome AF: 0.0000301

Gnomad4 SAS exome AF: 0.00193

Gnomad4 FIN exome AF: 0.0179

Gnomad4 NFE exome AF: 0.0220

Gnomad4 OTH exome AF: 0.0150

GnomAD4 genome AF: 0.0137 AC: 2081 AN: 152114 Hom.: 21 Cov.: 32 AF XY: 0.0134 AC XY: 995 AN XY: 74382

Gnomad4 AFR AF: 0.00342

Gnomad4 AMR AF: 0.0105

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0180 Hom.: 2

Bravo AF: 0.0131

Asia WGS AF: 0.00232 AC: 8 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.27
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: rs150888153; hg19: chr3-140681913;