8-103401496-G-T

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The NM_030780.5(SLC25A32):c.812+20C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00649 in 1,602,224 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0088 (14 hom., cov: 33)
  • Exomes 𝑓: 0.0062 (61 hom.)
• Consequence: SLC25A32 NM_030780.5 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0290

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 -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 8-103401496-G-T is Benign according to our data. Variant chr8-103401496-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1600030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A32	NM_030780.5	c.812+20C>A		intron_variant		ENST00000297578.9
SLC25A32	NR_102337.2	n.896+20C>A		intron_variant, non_coding_transcript_variant
SLC25A32	NR_102338.2	n.1091+20C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A32	ENST00000297578.9	c.812+20C>A		intron_variant		1	NM_030780.5	P1

Frequencies

GnomAD3 genomes AF: 0.00883 AC: 1343 AN: 152072 Hom.: 14 Cov.: 33

Gnomad AFR AF: 0.00676

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00425

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00673

Gnomad OTH AF: 0.0110

GnomAD3 exomes AF: 0.00840 AC: 2029 AN: 241618 Hom.: 24 AF XY: 0.00798 AC XY: 1043 AN XY: 130644

Gnomad AFR exome AF: 0.00859

Gnomad AMR exome AF: 0.00264

Gnomad ASJ exome AF: 0.00978

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00223

Gnomad FIN exome AF: 0.0403

Gnomad NFE exome AF: 0.00664

Gnomad OTH exome AF: 0.00963

GnomAD4 exome AF: 0.00625 AC: 9058 AN: 1450034 Hom.: 61 Cov.: 31 AF XY: 0.00620 AC XY: 4465 AN XY: 720704

Gnomad4 AFR exome AF: 0.00809

Gnomad4 AMR exome AF: 0.00313

Gnomad4 ASJ exome AF: 0.00909

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00237

Gnomad4 FIN exome AF: 0.0391

Gnomad4 NFE exome AF: 0.00515

Gnomad4 OTH exome AF: 0.00670

GnomAD4 genome AF: 0.00884 AC: 1345 AN: 152190 Hom.: 14 Cov.: 33 AF XY: 0.0102 AC XY: 761 AN XY: 74390

Gnomad4 AFR AF: 0.00677

Gnomad4 AMR AF: 0.00425

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.0443

Gnomad4 NFE AF: 0.00675

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.00750 Hom.: 1

Bravo AF: 0.00614

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 03, 2019	See Variant Classification Assertion Criteria. -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 22, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.57
Dann	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs59283978; hg19: chr8-104413724;