1-15736501-C-T

Variant names:

• chr1-15736501-C-T
• rs762087779
• NM_207348.3:c.16C>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_207348.3(SLC25A34):​c.16C>T​(p.Pro6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000846 in 1,300,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000085 (0 hom.)
• Consequence: SLC25A34 NM_207348.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.45
• Publications: 0 publications found

Genes affected

SLC25A34 (HGNC:27653): (solute carrier family 25 member 34) SLC25A34 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008]

ENSG00000237938 (HGNC:58402):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2741988).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207348.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A34	NM_207348.3	MANE Select	c.16C>T	p.Pro6Ser	missense	Exon 1 of 5	NP_997231.1	Q6PIV7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A34	ENST00000294454.6	TSL:1 MANE Select	c.16C>T	p.Pro6Ser	missense	Exon 1 of 5	ENSP00000294454.5	Q6PIV7
	SLC25A34	ENST00000949755.1		c.16C>T	p.Pro6Ser	missense	Exon 1 of 5	ENSP00000619814.1
	SLC25A34	ENST00000852312.1		c.16C>T	p.Pro6Ser	missense	Exon 1 of 4	ENSP00000522371.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.0000212 AC: 2 AN: 94558 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000182

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000846 AC: 11 AN: 1300952 Hom.: 0 Cov.: 31 AF XY: 0.00000949 AC XY: 6 AN XY: 632454

African (AFR) AF: 0.00 AC: 0 AN: 28132

American (AMR) AF: 0.0000961 AC: 2 AN: 20814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18742

East Asian (EAS) AF: 0.00 AC: 0 AN: 34110

South Asian (SAS) AF: 0.00 AC: 0 AN: 62876

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43094

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3584

European-Non Finnish (NFE) AF: 0.00000869 AC: 9 AN: 1036134

Other (OTH) AF: 0.00 AC: 0 AN: 53466

GnomAD4 genome Cov.: 33

ExAC AF: 0.00000882 AC: 1

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.042	T
BayesDel_noAF	Benign	-0.30
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.14	T
Eigen	Uncertain	0.32
Eigen_PC	Uncertain	0.23
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.79	T
M_CAP	Uncertain	0.13	D
MetaRNN	Benign	0.27	T
MetaSVM	Uncertain	0.076	D
MutationAssessor	Benign	1.3	L
PhyloP100		2.4
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-1.7	N
REVEL	Uncertain	0.37
Sift	Benign	0.10	T
Sift4G	Uncertain	0.019	D
Polyphen		0.98	D
Vest4		0.31
MutPred		0.42		Loss of glycosylation at T3 (P = 0.0456)
MVP		0.76
MPC		0.31
ClinPred		0.68	D
GERP RS		3.9
PromoterAI		0.00010	Neutral
Varity_R		0.15
gMVP		0.70
Mutation Taster		=69/31	polymorphism

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: rs762087779; hg19: chr1-16062996;