chr16-56636529-A-G

Variant names:

• chr16-56636529-A-G
• rs12051120
• ENST00000563395.5:n.200+25A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563395.5(MT1JP):​n.200+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 ENST00000563395.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 5 publications found

Genes affected

MT1JP (HGNC:):

MT1JP (HGNC:7402): (metallothionein 1J, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MT1JP	NR_036677.1	n.173+25A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT1JP	ENST00000563395.5	n.200+25A>G		intron_variant	Intron 2 of 2	1
MT1JP	ENST00000444023.4	n.94+25A>G		intron_variant	Intron 2 of 2	6
MT1JP	ENST00000564564.1	n.742+25A>G		intron_variant	Intron 1 of 1	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

GnomAD2 exomes AF: 0.0377 AC: 9471 AN: 251044 AF XY: 0.0339

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 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

African (AFR) AF: 0.155 AC: 5174 AN: 33470

American (AMR) AF: 0.0437 AC: 1954 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00784 AC: 205 AN: 26136

East Asian (EAS) AF: 0.0744 AC: 2952 AN: 39698

South Asian (SAS) AF: 0.0228 AC: 1964 AN: 86252

European-Finnish (FIN) AF: 0.0229 AC: 1221 AN: 53404

Middle Eastern (MID) AF: 0.0117 AC: 66 AN: 5652

European-Non Finnish (NFE) AF: 0.0206 AC: 22924 AN: 1111972

Other (OTH) AF: 0.0342 AC: 2064 AN: 60380

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

African (AFR) AF: 0.149 AC: 6177 AN: 41520

American (AMR) AF: 0.0382 AC: 585 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.0970 AC: 502 AN: 5176

South Asian (SAS) AF: 0.0260 AC: 125 AN: 4816

European-Finnish (FIN) AF: 0.0194 AC: 206 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0196 AC: 1332 AN: 68002

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0382 Hom.: 64

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

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