1-108138860-G-T

Position:

• chr1-108138860-G-T

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+198C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 152,220 control chromosomes in the GnomAD database, including 333 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.040 (333 hom., cov: 32)
• Consequence: SLC25A24 NM_013386.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.227

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=-0.87).
• BP6: Variant 1-108138860-G-T is Benign according to our data. Variant chr1-108138860-G-T is described in ClinVar as [Benign]. Clinvar id is 1252212.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A24	NM_013386.5	c.1249+198C>A		intron_variant		ENST00000565488.6
SLC25A24	NM_213651.3	c.1192+198C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A24	ENST00000565488.6	c.1249+198C>A		intron_variant		1	NM_013386.5	P1
SLC25A24	ENST00000370041.4	c.1192+198C>A		intron_variant		1
SLC25A24	ENST00000264128.13	c.*828+198C>A		intron_variant, NMD_transcript_variant		5
SLC25A24	ENST00000648874.1	c.*570+198C>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6072 AN: 152104 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0399 AC: 6075 AN: 152220 Hom.: 333 Cov.: 32 AF XY: 0.0437 AC XY: 3252 AN XY: 74418

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0370

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0782

Gnomad4 NFE AF: 0.0334

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0322 Hom.: 21

Bravo AF: 0.0367

Asia WGS AF: 0.154 AC: 533 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.35
DANN	Benign	0.39

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: rs11185282; hg19: chr1-108681482;