rs1865855

Positions:

• chr8-103404605-A-C

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.391+171T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,952 control chromosomes in the GnomAD database, including 1,303 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1303 hom., cov: 32)
• Consequence: SLC25A32 NM_030780.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.164

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=-0.95).
• BP6: Variant 8-103404605-A-C is Benign according to our data. Variant chr8-103404605-A-C is described in ClinVar as [Benign]. Clinvar id is 1279525.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A32	NM_030780.5	c.391+171T>G		intron_variant		ENST00000297578.9
SLC25A32	NR_102337.2	n.476-1281T>G		intron_variant, non_coding_transcript_variant
SLC25A32	NR_102338.2	n.670+171T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A32	ENST00000297578.9	c.391+171T>G		intron_variant		1	NM_030780.5	P1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19382 AN: 151834 Hom.: 1295 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0829

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.128 AC: 19412 AN: 151952 Hom.: 1303 Cov.: 32 AF XY: 0.128 AC XY: 9532 AN XY: 74254

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0829

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.126

Alfa AF: 0.137 Hom.: 778

Bravo AF: 0.132

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

Nov 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.40

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: rs1865855; hg19: chr8-104416833;