rs12818213

Positions:

• chr12-53678223-A-G
• chr12-53678223-A-T

Variant summary

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

The XM_047428989.1(ATP5MC2):​c.-32+3178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,068 control chromosomes in the GnomAD database, including 7,507 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 0.31 (7507 hom., cov: 32)
• Consequence: ATP5MC2 XM_047428989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

Genes affected

ATP5MC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP5MC2	XM_047428989.1	c.-32+3178T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47117 AN: 151950 Hom.: 7501 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.310 AC: 47140 AN: 152068 Hom.: 7507 Cov.: 32 AF XY: 0.307 AC XY: 22854 AN XY: 74344

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.313

Alfa AF: 0.301 Hom.: 1009

Bravo AF: 0.323

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12818213; hg19: chr12-54072007;