rs904773

Variant names:

• chr16-56617689-C-A
• rs904773
• ENST00000565768.4:n.315+99C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-56617689-C-A
• chr16-56617689-C-G
• chr16-56617689-C-T

Variant summary

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

The ENST00000565768.4(ENSG00000291105):​n.315+99C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 416,980 control chromosomes in the GnomAD database, including 132,533 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 0.80 (49136 hom., cov: 33)
  • Exomes 𝑓: 0.79 (83397 hom.)
• Consequence: ENSG00000291105 ENST00000565768.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 10 publications found

Genes affected

ENSG00000291105 (HGNC:):

MT1L (HGNC:7404): (metallothionein 1L (pseudogene)) Predicted to enable zinc ion binding activity. Involved in 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565768.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT1L	NR_001447.2		n.130+99C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291105	ENST00000565768.4	TSL:1	n.315+99C>A		intron	N/A
	ENSG00000291105	ENST00000849449.1		n.86C>A		non_coding_transcript_exon	Exon 1 of 3
	MT1L	ENST00000566367.2	TSL:6	n.28+99C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121955 AN: 152038 Hom.: 49095 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.806

GnomAD4 exome AF: 0.792 AC: 209822 AN: 264826 Hom.: 83397 AF XY: 0.795 AC XY: 120339 AN XY: 151444

African (AFR) AF: 0.836 AC: 5890 AN: 7044

American (AMR) AF: 0.681 AC: 15348 AN: 22522

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 4506 AN: 5612

East Asian (EAS) AF: 0.760 AC: 8706 AN: 11454

South Asian (SAS) AF: 0.807 AC: 39246 AN: 48642

European-Finnish (FIN) AF: 0.743 AC: 11468 AN: 15444

Middle Eastern (MID) AF: 0.809 AC: 869 AN: 1074

European-Non Finnish (NFE) AF: 0.809 AC: 114146 AN: 141010

Other (OTH) AF: 0.802 AC: 9643 AN: 12024

GnomAD4 genome AF: 0.802 AC: 122049 AN: 152154 Hom.: 49136 Cov.: 33 AF XY: 0.798 AC XY: 59314 AN XY: 74368

African (AFR) AF: 0.832 AC: 34530 AN: 41518

American (AMR) AF: 0.740 AC: 11309 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2760 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3891 AN: 5168

South Asian (SAS) AF: 0.817 AC: 3944 AN: 4830

European-Finnish (FIN) AF: 0.736 AC: 7776 AN: 10564

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55123 AN: 67992

Other (OTH) AF: 0.806 AC: 1703 AN: 2114

Alfa AF: 0.802 Hom.: 81553

Bravo AF: 0.800

Asia WGS AF: 0.786 AC: 2731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.34
DANN	Benign	0.30
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs904773; hg19: chr16-56651601;