rs964372

Variant names:

• chr16-56652118-C-A
• rs964372
• NM_005947.3:c.28+137C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-56652118-C-A
• chr16-56652118-C-G
• chr16-56652118-C-T

Variant summary

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

The NM_005947.3(MT1B):​c.28+137C>A 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: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MT1B NM_005947.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 18 publications found

Genes affected

MT1B (HGNC:7394): (metallothionein 1B) The protein encoded by this gene binds heavy metals and protects against toxicity from heavy metal ions. This gene is found in a cluster of similar genes on chromosome 16. [provided by RefSeq, Jul 2016]

ENSG00000259923 (HGNC:):

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
MT1B	NM_005947.3	c.28+137C>A		intron_variant	Intron 1 of 2	ENST00000334346.3	NP_005938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT1B	ENST00000334346.3	c.28+137C>A		intron_variant	Intron 1 of 2	1	NM_005947.3	ENSP00000334998.2
MT1B	ENST00000562399.1	c.28+137C>A		intron_variant	Intron 1 of 2	3		ENSP00000456056.1
ENSG00000259923	ENST00000568608.1	n.178+137C>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 905426 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 464008

African (AFR) AF: 0.00 AC: 0 AN: 22144

American (AMR) AF: 0.00 AC: 0 AN: 35484

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20592

East Asian (EAS) AF: 0.00 AC: 0 AN: 34896

South Asian (SAS) AF: 0.00 AC: 0 AN: 68560

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40372

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4612

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 636790

Other (OTH) AF: 0.00 AC: 0 AN: 41976

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.24
PhyloP100		-1.7
PromoterAI		-0.043	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs964372; hg19: chr16-56686030;