16-56670213-G-A

Variant names:

• chr16-56670213-G-A
• rs2062545
• NM_005951.2:c.29-293G>A

Variant summary

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

The NM_005951.2(MT1H):​c.29-293G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,208 control chromosomes in the GnomAD database, including 59,675 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 0.88 (59675 hom., cov: 32)
• Consequence: MT1H NM_005951.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 9 publications found

Genes affected

MT1H (HGNC:7400): (metallothionein 1H) Predicted to enable zinc ion binding activity. Involved in cellular response to cadmium ion and cellular response to zinc ion. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MT1H	NM_005951.2	c.29-293G>A		intron_variant	Intron 1 of 2	ENST00000332374.5	NP_005942.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT1H	ENST00000332374.5	c.29-293G>A		intron_variant	Intron 1 of 2	1	NM_005951.2	ENSP00000330587.5
MT1H	ENST00000569155.1	c.29-293G>A		intron_variant	Intron 1 of 1	1		ENSP00000457114.1

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133488 AN: 152090 Hom.: 59650 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.877 AC: 133562 AN: 152208 Hom.: 59675 Cov.: 32 AF XY: 0.881 AC XY: 65552 AN XY: 74438

African (AFR) AF: 0.684 AC: 28361 AN: 41474

American (AMR) AF: 0.934 AC: 14286 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 3221 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5174 AN: 5182

South Asian (SAS) AF: 0.942 AC: 4545 AN: 4824

European-Finnish (FIN) AF: 0.975 AC: 10363 AN: 10626

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.950 AC: 64619 AN: 68020

Other (OTH) AF: 0.903 AC: 1910 AN: 2114

Alfa AF: 0.914 Hom.: 116688

Bravo AF: 0.867

Asia WGS AF: 0.949 AC: 3300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.25
PromoterAI		-0.0094	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs2062545; hg19: chr16-56704125;