chr1-108136529-A-G

Position:

• chr1-108136529-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_013386.5(SLC25A24):​c.*124T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 737,958 control chromosomes in the GnomAD database, including 1,886 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.077 (618 hom., cov: 33)
  • Exomes 𝑓: 0.060 (1268 hom.)
• Consequence: SLC25A24 NM_013386.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.618

Genes affected

SLC25A24 (HGNC:20662): (solute carrier family 25 member 24) This gene encodes a carrier protein that transports ATP-Mg exchanging it for phosphate. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-108136529-A-G is Benign according to our data. Variant chr1-108136529-A-G is described in ClinVar as [Benign]. Clinvar id is 1240581.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A24	NM_013386.5	c.*124T>C		3_prime_UTR_variant	10/10	ENST00000565488.6
SLC25A24	NM_213651.3	c.*124T>C		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A24	ENST00000565488.6	c.*124T>C		3_prime_UTR_variant	10/10	1	NM_013386.5	P1
SLC25A24	ENST00000370041.4	c.*124T>C		3_prime_UTR_variant	10/10	1
SLC25A24	ENST00000264128.13	c.*1137T>C		3_prime_UTR_variant, NMD_transcript_variant	9/9	5
SLC25A24	ENST00000648874.1	c.*879T>C		3_prime_UTR_variant, NMD_transcript_variant	11/11

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11717 AN: 152174 Hom.: 614 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0865

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.0598 AC: 35049 AN: 585666 Hom.: 1268 Cov.: 8 AF XY: 0.0611 AC XY: 18678 AN XY: 305638

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.0370

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.000154

Gnomad4 SAS exome AF: 0.0862

Gnomad4 FIN exome AF: 0.0381

Gnomad4 NFE exome AF: 0.0595

Gnomad4 OTH exome AF: 0.0666

GnomAD4 genome AF: 0.0771 AC: 11741 AN: 152292 Hom.: 618 Cov.: 33 AF XY: 0.0749 AC XY: 5579 AN XY: 74488

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.0318

Gnomad4 NFE AF: 0.0590

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0710 Hom.: 174

Bravo AF: 0.0795

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.31
DANN	Benign	0.30

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: rs17021096; hg19: chr1-108679151;