rs2275716

chr10-68506789-G-T

Variant summary

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

The NM_152707.4(SLC25A16):c.224-71C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 925,650 control chromosomes in the GnomAD database, including 294,079 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 0.73 (41900 hom., cov: 32)
  • Exomes 𝑓: 0.80 (252179 hom.)
• Consequence: SLC25A16 NM_152707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

Genes affected

SLC25A16 (HGNC:10986): (solute carrier family 25 member 16) This gene encodes a protein that contains three tandemly repeated mitochondrial carrier protein domains. The encoded protein is localized in the inner membrane and facilitates the rapid transport and exchange of molecules between the cytosol and the mitochondrial matrix space. This gene has a possible role in Graves' disease. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A16	NM_152707.4	c.224-71C>A		intron_variant		ENST00000609923.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A16	ENST00000609923.6	c.224-71C>A		intron_variant		1	NM_152707.4	P1
SLC25A16	ENST00000493963.5	c.*152-71C>A		intron_variant, NMD_transcript_variant		1
SLC25A16	ENST00000491102.2	c.*127-71C>A		intron_variant, NMD_transcript_variant		4
SLC25A16	ENST00000265870.7	n.1229-71C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111381 AN: 151926 Hom.: 41901 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.722

GnomAD4 exome AF: 0.805 AC: 622455 AN: 773606 Hom.: 252179 AF XY: 0.800 AC XY: 316708 AN XY: 395740

Gnomad4 AFR exome AF: 0.592

Gnomad4 AMR exome AF: 0.593

Gnomad4 ASJ exome AF: 0.817

Gnomad4 EAS exome AF: 0.866

Gnomad4 SAS exome AF: 0.670

Gnomad4 FIN exome AF: 0.807

Gnomad4 NFE exome AF: 0.825

Gnomad4 OTH exome AF: 0.792

GnomAD4 genome AF: 0.733 AC: 111401 AN: 152044 Hom.: 41900 Cov.: 32 AF XY: 0.731 AC XY: 54335 AN XY: 74316

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.724

Alfa AF: 0.785 Hom.: 9706

Bravo AF: 0.714

Asia WGS AF: 0.716 AC: 2491 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.0
Dann	Benign	0.45

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: rs2275716; hg19: chr10-70266546;