8-103400160-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_030780.5(SLC25A32):c.*251G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 462,370 control chromosomes in the GnomAD database, including 48,066 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.46 (15990 hom., cov: 33)
  • Exomes 𝑓: 0.45 (32076 hom.)
• Consequence: SLC25A32 NM_030780.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.317

Genes affected

SLC25A32 (HGNC:29683): (solute carrier family 25 member 32) This gene encodes a member of the P(I/L)W subfamily of mitochondrial carrier family transport proteins. The encoded protein transports folate across the inner mitochondrial membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2013]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 8-103400160-C-A is Benign according to our data. Variant chr8-103400160-C-A is described in ClinVar as [Benign]. Clinvar id is 1256934.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A32	NM_030780.5	c.*251G>T		3_prime_UTR_variant	7/7	ENST00000297578.9
SLC25A32	NR_102337.2	n.1283G>T		non_coding_transcript_exon_variant	6/6
SLC25A32	NR_102338.2	n.1478G>T		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A32	ENST00000297578.9	c.*251G>T		3_prime_UTR_variant	7/7	1	NM_030780.5	P1

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69517 AN: 151888 Hom.: 15970 Cov.: 33

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.475

GnomAD4 exome AF: 0.449 AC: 139311 AN: 310364 Hom.: 32076 Cov.: 3 AF XY: 0.445 AC XY: 72641 AN XY: 163134

Gnomad4 AFR exome AF: 0.495

Gnomad4 AMR exome AF: 0.398

Gnomad4 ASJ exome AF: 0.512

Gnomad4 EAS exome AF: 0.372

Gnomad4 SAS exome AF: 0.411

Gnomad4 FIN exome AF: 0.484

Gnomad4 NFE exome AF: 0.456

Gnomad4 OTH exome AF: 0.448

GnomAD4 genome AF: 0.458 AC: 69573 AN: 152006 Hom.: 15990 Cov.: 33 AF XY: 0.458 AC XY: 34044 AN XY: 74282

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.471

Alfa AF: 0.454 Hom.: 32022

Bravo AF: 0.453

Asia WGS AF: 0.393 AC: 1365 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 31, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.17
Dann	Benign	0.42

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: rs2241777; hg19: chr8-104412388;