15-51203633-A-G

Variant names:

• chr15-51203633-A-G
• rs934632
• ENST00000559909.1:n.195-74350A>G

Variant summary

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

The ENST00000559909.1(MIR4713HG):​n.195-74350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,078 control chromosomes in the GnomAD database, including 47,473 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 0.79 (47473 hom., cov: 31)
• Consequence: MIR4713HG ENST00000559909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 4 publications found

Genes affected

MIR4713HG (HGNC:53124): (MIR4713 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559909.1. 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
	MIR4713HG	NR_146310.1		n.195-74350A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4713HG	ENST00000559909.1	TSL:4	n.195-74350A>G		intron	N/A
	MIR4713HG	ENST00000805692.1		n.279-74350A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119864 AN: 151960 Hom.: 47449 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.789 AC: 119936 AN: 152078 Hom.: 47473 Cov.: 31 AF XY: 0.789 AC XY: 58636 AN XY: 74338

African (AFR) AF: 0.755 AC: 31289 AN: 41452

American (AMR) AF: 0.748 AC: 11428 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2987 AN: 3472

East Asian (EAS) AF: 0.693 AC: 3584 AN: 5170

South Asian (SAS) AF: 0.797 AC: 3833 AN: 4812

European-Finnish (FIN) AF: 0.804 AC: 8520 AN: 10594

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55745 AN: 67976

Other (OTH) AF: 0.775 AC: 1639 AN: 2114

Alfa AF: 0.809 Hom.: 111028

Bravo AF: 0.781

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.40
PhyloP100		-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: rs934632;

hg19: chr15-51495830;