rs2275716

Variant names:

• chr10-68506789-G-T
• rs2275716
• NM_152707.4:c.224-71C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC25A16	NM_152707.4	c.224-71C>A		intron_variant	Intron 2 of 8	ENST00000609923.6	NP_689920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A16	ENST00000609923.6	c.224-71C>A		intron_variant	Intron 2 of 8	1	NM_152707.4	ENSP00000476815.1

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

African (AFR) AF: 0.592 AC: 10005 AN: 16902

American (AMR) AF: 0.593 AC: 9681 AN: 16312

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 13270 AN: 16252

East Asian (EAS) AF: 0.866 AC: 26105 AN: 30132

South Asian (SAS) AF: 0.670 AC: 32076 AN: 47842

European-Finnish (FIN) AF: 0.807 AC: 30580 AN: 37894

Middle Eastern (MID) AF: 0.766 AC: 1944 AN: 2538

European-Non Finnish (NFE) AF: 0.825 AC: 470595 AN: 570146

Other (OTH) AF: 0.792 AC: 28199 AN: 35588

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

African (AFR) AF: 0.589 AC: 24432 AN: 41478

American (AMR) AF: 0.638 AC: 9722 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2862 AN: 3470

East Asian (EAS) AF: 0.844 AC: 4357 AN: 5162

South Asian (SAS) AF: 0.655 AC: 3159 AN: 4820

European-Finnish (FIN) AF: 0.798 AC: 8427 AN: 10562

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55861 AN: 68008

Other (OTH) AF: 0.724 AC: 1523 AN: 2104

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
PhyloP100		0.23
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: rs2275716; hg19: chr10-70266546;