Variant rs17105087 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_030631.4(SLC25A21):c.441A>G(p.Gln147Gln) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 1,613,042 control chromosomes in the GnomAD database, including 11,499 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1298 hom., cov: 32)

Exomes 𝑓: 0.085 ( 10201 hom. )

Consequence

SLC25A21
NM_030631.4 splice_region, synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.08

Variant links:

Genes affected

SLC25A21 (HGNC:14411): (solute carrier family 25 member 21) SLC25A21 is a homolog of the S. cerevisiae ODC proteins, mitochondrial carriers that transport C5-C7 oxodicarboxylates across inner mitochondrial membranes. One of the species transported by ODC is 2-oxoadipate, a common intermediate in the catabolism of lysine, tryptophan, and hydroxylysine in mammals. Within mitochondria, 2-oxoadipate is converted into acetyl-CoA.[supplied by OMIM, Apr 2004]

SLC25A21 links:

SLC25A21 (HGNC:):

SLC25A21 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 14-36711480-T-C is Benign according to our data. Variant chr14-36711480-T-C is described in ClinVar as [Benign]. Clinvar id is 1332980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A21	NM_030631.4 linkuse as main transcript	c.441A>G	p.Gln147Gln	splice_region_variant, synonymous_variant	7/10	ENST00000331299.6	NP_085134.1	Q9BQT8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC25A21	ENST00000331299.6 linkuse as main transcript	c.441A>G	p.Gln147Gln	splice_region_variant, synonymous_variant	7/10	1	NM_030631.4	ENSP00000329452.5	Q9BQT8-1
SLC25A21	ENST00000555449.5 linkuse as main transcript	c.441A>G	p.Gln147Gln	splice_region_variant, synonymous_variant	7/11	2		ENSP00000451873.1	Q9BQT8-2
SLC25A21	ENST00000556444.1 linkuse as main transcript	n.113A>G		splice_region_variant, non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15536

AN:

152010

Hom.:

1295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.0912

Gnomad AMR

AF:

0.0960

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.488

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0604

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.129

AC:

32343

AN:

250256

Hom.:

3918

AF XY:

0.130

AC XY:

17542

AN XY:

135230

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.108

Gnomad ASJ exome

AF:

0.140

Gnomad EAS exome

AF:

0.500

Gnomad SAS exome

AF:

0.209

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.0624

Gnomad OTH exome

AF:

0.109

GnomAD4 exome

AF:

0.0849

AC:

124090

AN:

1460914

Hom.:

10201

Cov.:

AF XY:

0.0884

AC XY:

64231

AN XY:

726732

show subpopulations

Gnomad4 AFR exome

AF:

0.112

Gnomad4 AMR exome

AF:

0.105

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.480

Gnomad4 SAS exome

AF:

0.206

Gnomad4 FIN exome

AF:

0.0974

Gnomad4 NFE exome

AF:

0.0565

Gnomad4 OTH exome

AF:

0.108

GnomAD4 genome

AF:

0.102

AC:

15558

AN:

152128

Hom.:

1298

Cov.:

AF XY:

0.109

AC XY:

8077

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.0960

Gnomad4 ASJ

AF:

0.139

Gnomad4 EAS

AF:

0.487

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.0604

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.0743

Hom.:

849

Bravo

AF:

0.103

Asia WGS

AF:

0.331

AC:

1148

AN:

3476

EpiCase

AF:

0.0652

EpiControl

AF:

0.0665

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Mitochondrial DNA depletion syndrome 18

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.86

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.86

Position offset: -1

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