19-58559954-C-T

Variant names:

• chr19-58559954-C-T
• rs10413586
• ENST00000600534.1:n.185+545C>T

Variant summary

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

The ENST00000692455.3(MZF1-AS1):​n.1364C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,246 control chromosomes in the GnomAD database, including 37,865 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 0.69 (37865 hom., cov: 35)
• Consequence: MZF1-AS1 ENST00000692455.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 17 publications found

Genes affected

MZF1-AS1 (HGNC:51271): (MZF1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692455.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MZF1-AS1	NR_027334.2		n.224+545C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MZF1-AS1	ENST00000600534.1	TSL:1	n.185+545C>T		intron	N/A
	MZF1-AS1	ENST00000692455.3		n.1364C>T		non_coding_transcript_exon	Exon 1 of 1
	MZF1-AS1	ENST00000789879.1		n.556C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105098 AN: 152130 Hom.: 37803 Cov.: 35

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.691 AC: 105218 AN: 152246 Hom.: 37865 Cov.: 35 AF XY: 0.692 AC XY: 51495 AN XY: 74410

African (AFR) AF: 0.901 AC: 37481 AN: 41580

American (AMR) AF: 0.686 AC: 10479 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1781 AN: 3468

East Asian (EAS) AF: 0.791 AC: 4101 AN: 5182

South Asian (SAS) AF: 0.650 AC: 3136 AN: 4824

European-Finnish (FIN) AF: 0.657 AC: 6955 AN: 10586

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39203 AN: 68004

Other (OTH) AF: 0.634 AC: 1341 AN: 2114

Alfa AF: 0.603 Hom.: 35075

Bravo AF: 0.701

Asia WGS AF: 0.779 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.33
PhyloP100		-0.10
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10413586;

hg19: chr19-59071321;