rs12900916

Positions:

• chr15-51043166-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146310.1(MIR4713HG):​n.194+5485A>G variant causes a intron, non coding transcript 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 NR_146310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MIR4713HG	NR_146310.1	n.194+5485A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.194+5485A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.331

Alfa AF: 0.365 Hom.: 17545

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12900916; hg19: chr15-51335363;