8-103401273-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.812+243G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0522 in 152,060 control chromosomes in the GnomAD database, including 270 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.052 (270 hom., cov: 33)
• Consequence: SLC25A32 NM_030780.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.249

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=-0.86).
• BP6: Variant 8-103401273-C-T is Benign according to our data. Variant chr8-103401273-C-T is described in ClinVar as [Benign]. Clinvar id is 1267556.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A32	NM_030780.5	c.812+243G>A		intron_variant		ENST00000297578.9
SLC25A32	NR_102337.2	n.896+243G>A		intron_variant, non_coding_transcript_variant
SLC25A32	NR_102338.2	n.1091+243G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A32	ENST00000297578.9	c.812+243G>A		intron_variant		1	NM_030780.5	P1

Frequencies

GnomAD3 genomes AF: 0.0522 AC: 7934 AN: 151942 Hom.: 270 Cov.: 33

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.00713

Gnomad SAS AF: 0.0152

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0783

Gnomad OTH AF: 0.0672

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0522 AC: 7932 AN: 152060 Hom.: 270 Cov.: 33 AF XY: 0.0503 AC XY: 3740 AN XY: 74326

Gnomad4 AFR AF: 0.0200

Gnomad4 AMR AF: 0.0512

Gnomad4 ASJ AF: 0.0525

Gnomad4 EAS AF: 0.00714

Gnomad4 SAS AF: 0.0152

Gnomad4 FIN AF: 0.0487

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.0660

Alfa AF: 0.0614 Hom.: 40

Bravo AF: 0.0516

Asia WGS AF: 0.0130 AC: 45 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

Sep 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.5
Dann	Benign	0.65

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: rs117366417; hg19: chr8-104413501;