rs11644094

Variant names:

• chr16-56590167-A-C
• rs11644094
• NM_005954.4:c.97+232A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-56590167-A-C
• chr16-56590167-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005954.4(MT3):​c.97+232A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MT3 NM_005954.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 11 publications found

Genes affected

MT3 (HGNC:7408): (metallothionein 3) This gene is a member of the metallothionein family of genes. Proteins encoded by this gene family are low in molecular weight, are cysteine-rich, lack aromatic residues, and bind divalent heavy metal ions. This gene family member displays tissue-specific expression, and contains a threonine insert near its N-terminus and a glutamate-rich hexapeptide insert near its C-terminus relative to the proteins encoded by other gene family members. It plays an important role in zinc and copper homeostasis, and is induced under hypoxic conditions. The encoded protein is a growth inhibitory factor, and reduced levels of the protein are observed in the brains of individuals with some metal-linked neurodegenerative disorders such as Alzheimer's disease. [provided by RefSeq, Sep 2017]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MT3	NM_005954.4	c.97+232A>C		intron_variant	Intron 2 of 2	ENST00000200691.5	NP_005945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT3	ENST00000200691.5	c.97+232A>C		intron_variant	Intron 2 of 2	1	NM_005954.4	ENSP00000200691.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 521832 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 279058

African (AFR) AF: 0.00 AC: 0 AN: 15154

American (AMR) AF: 0.00 AC: 0 AN: 32860

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18320

East Asian (EAS) AF: 0.00 AC: 0 AN: 31650

South Asian (SAS) AF: 0.00 AC: 0 AN: 59186

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32286

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3824

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 299382

Other (OTH) AF: 0.00 AC: 0 AN: 29170

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 9669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-0.82

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

Other links and lift over

dbSNP: rs11644094; hg19: chr16-56624079;