19-6451422-G-A

Variant names:

• chr19-6451422-G-A
• rs7247153
• NM_024103.3:c.1071+890C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024103.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A23	NM_024103.3	MANE Select	c.1071+890C>T		intron	N/A	NP_077008.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A23	ENST00000301454.9	TSL:1 MANE Select	c.1071+890C>T		intron	N/A	ENSP00000301454.3
	SLC25A23	ENST00000334510.9	TSL:1	c.1071+890C>T		intron	N/A	ENSP00000334537.4
	SLC25A23	ENST00000264088.8	TSL:1	n.1212+890C>T		intron	N/A	ENSP00000264088.3

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

African (AFR) AF: 0.730 AC: 30262 AN: 41464

American (AMR) AF: 0.310 AC: 4732 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1594 AN: 5184

South Asian (SAS) AF: 0.348 AC: 1682 AN: 4828

European-Finnish (FIN) AF: 0.449 AC: 4733 AN: 10546

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26802 AN: 67980

Other (OTH) AF: 0.421 AC: 884 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.80
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7247153; hg19: chr19-6451433;