Variant 8-103400407-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000297578.9(SLC25A32):c.*4C>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 0.0272 in 1,613,758 control chromosomes in the GnomAD database, including 782 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.020 ( 59 hom., cov: 33)

Exomes 𝑓: 0.028 ( 723 hom. )

Consequence

SLC25A32
ENST00000297578.9 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0170

Variant links:

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]

SLC25A32 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 8-103400407-G-A is Benign according to our data. Variant chr8-103400407-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316181.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0197 (2994/152280) while in subpopulation NFE AF= 0.0321 (2186/68020). AF 95% confidence interval is 0.031. There are 59 homozygotes in gnomad4. There are 1390 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 59 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
SLC25A32	NM_030780.5 linkuse as main transcript	c.*4C>T	3_prime_UTR_variant	7/7	ENST00000297578.9	NP_110407.2
SLC25A32	NR_102337.2 linkuse as main transcript	n.1036C>T	non_coding_transcript_exon_variant	6/6
SLC25A32	NR_102338.2 linkuse as main transcript	n.1231C>T	non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A32	ENST00000297578.9 linkuse as main transcript	c.*4C>T		3_prime_UTR_variant	7/7	1	NM_030780.5	ENSP00000297578	P1

Frequencies

GnomAD3 genomes

AF:

0.0197

AC:

2995

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00579

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0190

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.0145

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0321

Gnomad OTH

AF:

0.0230

GnomAD3 exomes

AF:

0.0190

AC:

4762

AN:

251240

Hom.:

AF XY:

0.0190

AC XY:

2582

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.00560

Gnomad AMR exome

AF:

0.0136

Gnomad ASJ exome

AF:

0.00953

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00722

Gnomad FIN exome

AF:

0.0134

Gnomad NFE exome

AF:

0.0304

Gnomad OTH exome

AF:

0.0217

GnomAD4 exome

AF:

0.0280

AC:

40939

AN:

1461478

Hom.:

723

Cov.:

AF XY:

0.0274

AC XY:

19910

AN XY:

727042

show subpopulations

Gnomad4 AFR exome

AF:

0.00475

Gnomad4 AMR exome

AF:

0.0144

Gnomad4 ASJ exome

AF:

0.00972

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00768

Gnomad4 FIN exome

AF:

0.0133

Gnomad4 NFE exome

AF:

0.0333

Gnomad4 OTH exome

AF:

0.0245

GnomAD4 genome

AF:

0.0197

AC:

2994

AN:

152280

Hom.:

Cov.:

AF XY:

0.0187

AC XY:

1390

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00577

Gnomad4 AMR

AF:

0.0190

Gnomad4 ASJ

AF:

0.00893

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00559

Gnomad4 FIN

AF:

0.0145

Gnomad4 NFE

AF:

0.0321

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.0196

Hom.:

Bravo

AF:

0.0196

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0312

EpiControl

AF:

0.0311

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 28, 2021	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

SLC25A32-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 13, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

7.1

DANN

Benign

0.70

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over