rs7196890

chr16-56637108-C-Achr16-56637108-C-G

Variant summary

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

The 16-56637108-C-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 568,024 control chromosomes in the GnomAD database, including 36,226 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 0.34 (9038 hom., cov: 33)
  • Exomes 𝑓: 0.36 (27188 hom.)
• Consequence: MT1JP NR_036677.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.90

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MT1JP	NR_036677.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT1JP	ENST00000563395.4			downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52020 AN: 151844 Hom.: 9028 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.355 AC: 147734 AN: 416062 Hom.: 27188 Cov.: 5 AF XY: 0.361 AC XY: 78565 AN XY: 217912

Gnomad4 AFR exome AF: 0.323

Gnomad4 AMR exome AF: 0.332

Gnomad4 ASJ exome AF: 0.381

Gnomad4 EAS exome AF: 0.373

Gnomad4 SAS exome AF: 0.461

Gnomad4 FIN exome AF: 0.303

Gnomad4 NFE exome AF: 0.342

Gnomad4 OTH exome AF: 0.356

GnomAD4 genome AF: 0.343 AC: 52054 AN: 151962 Hom.: 9038 Cov.: 33 AF XY: 0.342 AC XY: 25384 AN XY: 74232

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.355

Alfa AF: 0.311 Hom.: 2662

Bravo AF: 0.339

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.090
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7196890; hg19: chr16-56671020;