rs16964189

Variant names:

• chr15-51202040-C-T
• rs16964189
• ENST00000559909.1:n.195-75943C>T

Variant summary

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

The ENST00000559909.1(MIR4713HG):​n.195-75943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,106 control chromosomes in the GnomAD database, including 3,091 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 0.20 (3091 hom., cov: 32)
• Consequence: MIR4713HG ENST00000559909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 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.195-75943C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4713HG	ENST00000559909.1	TSL:4	n.195-75943C>T		intron	N/A
	MIR4713HG	ENST00000805692.1		n.279-75943C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30502 AN: 151990 Hom.: 3089 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 30512 AN: 152106 Hom.: 3091 Cov.: 32 AF XY: 0.202 AC XY: 15050 AN XY: 74368

African (AFR) AF: 0.187 AC: 7763 AN: 41486

American (AMR) AF: 0.175 AC: 2683 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3468

East Asian (EAS) AF: 0.158 AC: 819 AN: 5182

South Asian (SAS) AF: 0.289 AC: 1390 AN: 4810

European-Finnish (FIN) AF: 0.196 AC: 2075 AN: 10574

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14316 AN: 67978

Other (OTH) AF: 0.199 AC: 420 AN: 2108

Alfa AF: 0.205 Hom.: 8499

Bravo AF: 0.194

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		0.024

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: rs16964189;

hg19: chr15-51494237;