15-51180048-C-T

Variant names:

• chr15-51180048-C-T
• rs1122044
• ENST00000559909.1:n.195-97935C>T

Variant summary

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

The ENST00000559909.1(MIR4713HG):​n.195-97935C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,062 control chromosomes in the GnomAD database, including 26,927 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 0.58 (26927 hom., cov: 32)
• Consequence: MIR4713HG ENST00000559909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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.195-97935C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4713HG	ENST00000559909.1	TSL:4	n.195-97935C>T		intron	N/A
	MIR4713HG	ENST00000805692.1		n.279-97935C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88223 AN: 151944 Hom.: 26886 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.581 AC: 88317 AN: 152062 Hom.: 26927 Cov.: 32 AF XY: 0.580 AC XY: 43109 AN XY: 74338

African (AFR) AF: 0.743 AC: 30811 AN: 41480

American (AMR) AF: 0.524 AC: 8006 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1237 AN: 3468

East Asian (EAS) AF: 0.858 AC: 4447 AN: 5180

South Asian (SAS) AF: 0.427 AC: 2055 AN: 4814

European-Finnish (FIN) AF: 0.571 AC: 6027 AN: 10558

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33944 AN: 67982

Other (OTH) AF: 0.528 AC: 1111 AN: 2106

Alfa AF: 0.510 Hom.: 10637

Bravo AF: 0.590

Asia WGS AF: 0.627 AC: 2179 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	0.94
DANN	Benign	0.78
PhyloP100		-0.11

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: rs1122044;

hg19: chr15-51472245;