chr1-108138978-T-C

Position:

• chr1-108138978-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_013386.5(SLC25A24):​c.1249+80A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,345,962 control chromosomes in the GnomAD database, including 31,900 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.19 (3016 hom., cov: 32)
  • Exomes 𝑓: 0.22 (28884 hom.)
• Consequence: SLC25A24 NM_013386.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.157

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-108138978-T-C is Benign according to our data. Variant chr1-108138978-T-C is described in ClinVar as [Benign]. Clinvar id is 1276686.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A24	NM_013386.5	c.1249+80A>G		intron_variant		ENST00000565488.6
SLC25A24	NM_213651.3	c.1192+80A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A24	ENST00000565488.6	c.1249+80A>G		intron_variant		1	NM_013386.5	P1
SLC25A24	ENST00000370041.4	c.1192+80A>G		intron_variant		1
SLC25A24	ENST00000264128.13	c.*828+80A>G		intron_variant, NMD_transcript_variant		5
SLC25A24	ENST00000648874.1	c.*570+80A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29051 AN: 152060 Hom.: 3018 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.216 AC: 258084 AN: 1193784 Hom.: 28884 AF XY: 0.216 AC XY: 125794 AN XY: 583300

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.241

Gnomad4 ASJ exome AF: 0.180

Gnomad4 EAS exome AF: 0.0974

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.239

Gnomad4 NFE exome AF: 0.226

Gnomad4 OTH exome AF: 0.203

GnomAD4 genome AF: 0.191 AC: 29053 AN: 152178 Hom.: 3016 Cov.: 32 AF XY: 0.189 AC XY: 14080 AN XY: 74380

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0948

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.213

Alfa AF: 0.206 Hom.: 668

Bravo AF: 0.190

Asia WGS AF: 0.121 AC: 421 AN: 3478

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

May 16, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs34563977; hg19: chr1-108681600; COSMIC: COSV51450664;