rs1861956

chr17-8295368-C-T

Variant summary

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

The NM_001320870.2(SLC25A35):c.-561G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 985,354 control chromosomes in the GnomAD database, including 64,576 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 0.32 (7740 hom., cov: 32)
  • Exomes 𝑓: 0.37 (56836 hom.)
• Consequence: SLC25A35 NM_001320870.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

SLC25A35 (HGNC:31921): (solute carrier family 25 member 35) SLC25A35 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A35	NM_001320870.2	c.-561G>A		5_prime_UTR_variant	1/5	ENST00000577745.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A35	ENST00000577745.2	c.-561G>A		5_prime_UTR_variant	1/5	1	NM_001320870.2	P1
SLC25A35	ENST00000579192.5			upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47965 AN: 151916 Hom.: 7729 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.322

GnomAD4 exome AF: 0.369 AC: 307087 AN: 833320 Hom.: 56836 Cov.: 31 AF XY: 0.369 AC XY: 142189 AN XY: 384886

Gnomad4 AFR exome AF: 0.272

Gnomad4 AMR exome AF: 0.254

Gnomad4 ASJ exome AF: 0.331

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.322

Gnomad4 FIN exome AF: 0.288

Gnomad4 NFE exome AF: 0.374

Gnomad4 OTH exome AF: 0.335

GnomAD4 genome AF: 0.316 AC: 48003 AN: 152034 Hom.: 7740 Cov.: 32 AF XY: 0.309 AC XY: 22965 AN XY: 74326

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.319

Alfa AF: 0.341 Hom.: 1972

Bravo AF: 0.317

Asia WGS AF: 0.278 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	9.9
Dann	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1861956; hg19: chr17-8198686; COSMIC: COSV66295038;