rs7189840

Variant names:

• chr16-56649714-G-A
• rs7189840
• ENST00000568608.1:n.124+710G>A

Variant summary

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

The ENST00000568608.1(ENSG00000259923):​n.124+710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,046 control chromosomes in the GnomAD database, including 17,819 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 0.48 (17819 hom., cov: 33)
• Consequence: ENSG00000259923 ENST00000568608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

ENSG00000259923 (HGNC:):

MT1CP (HGNC:7395): (metallothionein 1C, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259923	ENST00000568608.1	n.124+710G>A		intron_variant	Intron 1 of 2	5
MT1CP	ENST00000567054.1	n.*200G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73244 AN: 151928 Hom.: 17798 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.482 AC: 73295 AN: 152046 Hom.: 17819 Cov.: 33 AF XY: 0.486 AC XY: 36089 AN XY: 74320

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.461

Alfa AF: 0.477 Hom.: 35741

Bravo AF: 0.476

Asia WGS AF: 0.540 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7189840; hg19: chr16-56683626;