8-103400602-C-T

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.813-56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 1,581,770 control chromosomes in the GnomAD database, including 7,731 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.071 (490 hom., cov: 33)
  • Exomes 𝑓: 0.096 (7241 hom.)
• Consequence: SLC25A32 NM_030780.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.922

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=-0.83).
• BP6: Variant 8-103400602-C-T is Benign according to our data. Variant chr8-103400602-C-T is described in ClinVar as [Benign]. Clinvar id is 1241405.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A32	NM_030780.5	c.813-56G>A		intron_variant		ENST00000297578.9
SLC25A32	NR_102337.2	n.897-56G>A		intron_variant, non_coding_transcript_variant
SLC25A32	NR_102338.2	n.1092-56G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A32	ENST00000297578.9	c.813-56G>A		intron_variant		1	NM_030780.5	P1

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10725 AN: 152080 Hom.: 491 Cov.: 33

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0606

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00905

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0998

Gnomad OTH AF: 0.0818

GnomAD4 exome AF: 0.0964 AC: 137858 AN: 1429572 Hom.: 7241 AF XY: 0.0964 AC XY: 68646 AN XY: 712258

Gnomad4 AFR exome AF: 0.0148

Gnomad4 AMR exome AF: 0.0438

Gnomad4 ASJ exome AF: 0.118

Gnomad4 EAS exome AF: 0.00600

Gnomad4 SAS exome AF: 0.0823

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.104

Gnomad4 OTH exome AF: 0.0935

GnomAD4 genome AF: 0.0705 AC: 10730 AN: 152198 Hom.: 490 Cov.: 33 AF XY: 0.0709 AC XY: 5273 AN XY: 74402

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.0606

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00907

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.0997

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0879 Hom.: 131

Bravo AF: 0.0661

Asia WGS AF: 0.0400 AC: 140 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	-0.83
Cadd	Benign	0.88
Dann	Benign	0.79

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: rs10103739; hg19: chr8-104412830;