rs12051120

Positions:

• chr16-56636529-A-G

Variant summary

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

The ENST00000563395.4(MT1JP):​n.173+25A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0295 in 1,613,904 control chromosomes in the GnomAD database, including 1,492 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 0.060 (536 hom., cov: 34)
  • Exomes 𝑓: 0.026 (956 hom.)
• Consequence: MT1JP ENST00000563395.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

MT1JP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MT1JP	NR_036677.1	n.173+25A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT1JP	ENST00000563395.4	n.173+25A>G		intron_variant		1
MT1JP	ENST00000444023.4	n.94+25A>G		intron_variant		6
MT1JP	ENST00000564564.1	n.742+25A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0595 AC: 9051 AN: 152104 Hom.: 534 Cov.: 34

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0194

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0484

GnomAD3 exomes AF: 0.0377 AC: 9471 AN: 251044 Hom.: 366 AF XY: 0.0339 AC XY: 4607 AN XY: 135784

Gnomad AFR exome AF: 0.152

Gnomad AMR exome AF: 0.0464

Gnomad ASJ exome AF: 0.00755

Gnomad EAS exome AF: 0.102

Gnomad SAS exome AF: 0.0213

Gnomad FIN exome AF: 0.0221

Gnomad NFE exome AF: 0.0190

Gnomad OTH exome AF: 0.0286

GnomAD4 exome AF: 0.0264 AC: 38524 AN: 1461684 Hom.: 956 Cov.: 32 AF XY: 0.0256 AC XY: 18606 AN XY: 727142

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.0437

Gnomad4 ASJ exome AF: 0.00784

Gnomad4 EAS exome AF: 0.0744

Gnomad4 SAS exome AF: 0.0228

Gnomad4 FIN exome AF: 0.0229

Gnomad4 NFE exome AF: 0.0206

Gnomad4 OTH exome AF: 0.0342

GnomAD4 genome AF: 0.0596 AC: 9069 AN: 152220 Hom.: 536 Cov.: 34 AF XY: 0.0578 AC XY: 4302 AN XY: 74436

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0382

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.0260

Gnomad4 FIN AF: 0.0194

Gnomad4 NFE AF: 0.0196

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0350 Hom.: 55

Bravo AF: 0.0667

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12051120; hg19: chr16-56670441; COSMIC: COSV51947307;