rs7247153

Positions:

• chr19-6451422-G-A
• chr19-6451422-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024103.3(SLC25A23):​c.1071+890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,036 control chromosomes in the GnomAD database, including 19,120 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (19120 hom., cov: 33)
• Consequence: SLC25A23 NM_024103.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

Genes affected

SLC25A23 (HGNC:19375): (solute carrier family 25 member 23) Predicted to enable ATP transmembrane transporter activity. Involved in calcium import into the mitochondrion; positive regulation of mitochondrial calcium ion concentration; and regulation of cellular hyperosmotic salinity response. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A23	NM_024103.3	c.1071+890C>T		intron_variant		ENST00000301454.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A23	ENST00000301454.9	c.1071+890C>T		intron_variant		1	NM_024103.3	P1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71777 AN: 151918 Hom.: 19068 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.473 AC: 71889 AN: 152036 Hom.: 19120 Cov.: 33 AF XY: 0.469 AC XY: 34856 AN XY: 74308

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.421

Alfa AF: 0.411 Hom.: 2219

Bravo AF: 0.470

Asia WGS AF: 0.379 AC: 1317 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.80

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: rs7247153; hg19: chr19-6451433;