rs12900916

Variant names:

• chr15-51043166-A-G
• rs12900916
• ENST00000559909.1:n.194+5485A>G

Variant summary

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

The ENST00000559909.1(MIR4713HG):​n.194+5485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,964 control chromosomes in the GnomAD database, including 7,831 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 0.31 (7831 hom., cov: 31)
• Consequence: MIR4713HG ENST00000559909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4713HG	NR_146310.1	n.194+5485A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.194+5485A>G		intron_variant	Intron 1 of 2	4
MIR4713HG	ENST00000805692.1	n.278+5485A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47082 AN: 151846 Hom.: 7821 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.310 AC: 47144 AN: 151964 Hom.: 7831 Cov.: 31 AF XY: 0.308 AC XY: 22887 AN XY: 74292

African (AFR) AF: 0.216 AC: 8962 AN: 41436

American (AMR) AF: 0.247 AC: 3771 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1571 AN: 3470

East Asian (EAS) AF: 0.143 AC: 738 AN: 5168

South Asian (SAS) AF: 0.390 AC: 1872 AN: 4806

European-Finnish (FIN) AF: 0.323 AC: 3412 AN: 10550

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25692 AN: 67942

Other (OTH) AF: 0.331 AC: 698 AN: 2110

Alfa AF: 0.354 Hom.: 36925

Bravo AF: 0.292

Asia WGS AF: 0.293 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.73
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs12900916; hg19: chr15-51335363;