rs6752812

Positions:

• chr2-171986588-C-A

Variant summary

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

The ENST00000472748.5(SLC25A12):​n.177+13091G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,008 control chromosomes in the GnomAD database, including 6,222 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 0.28 (6222 hom., cov: 33)
• Consequence: SLC25A12 ENST00000472748.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

Genes affected

SLC25A12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905590	XR_007087296.1	n.327+4759G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A12	ENST00000464063.1	n.181+13091G>T		intron_variant		4
SLC25A12	ENST00000472748.5	n.177+13091G>T		intron_variant		3
SLC25A12	ENST00000484227.5	n.210+4759G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42805 AN: 151888 Hom.: 6219 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.282 AC: 42821 AN: 152008 Hom.: 6222 Cov.: 33 AF XY: 0.275 AC XY: 20445 AN XY: 74306

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.286

Alfa AF: 0.295 Hom.: 2661

Bravo AF: 0.284

Asia WGS AF: 0.227 AC: 789 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6752812; hg19: chr2-172851502;