rs4775919

Variant names:

• chr15-51153712-G-A
• rs4775919
• ENST00000559909.1:n.194+116031G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-51153712-G-A
• chr15-51153712-G-C
• chr15-51153712-G-T

Variant summary

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

The ENST00000559909.1(MIR4713HG):​n.194+116031G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,044 control chromosomes in the GnomAD database, including 53,013 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 0.83 (53013 hom., cov: 30)
• Consequence: MIR4713HG ENST00000559909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 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.194+116031G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4713HG	ENST00000559909.1	TSL:4	n.194+116031G>A		intron	N/A
	MIR4713HG	ENST00000805692.1		n.278+116031G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126568 AN: 151926 Hom.: 52956 Cov.: 30

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.833 AC: 126688 AN: 152044 Hom.: 53013 Cov.: 30 AF XY: 0.833 AC XY: 61939 AN XY: 74320

African (AFR) AF: 0.815 AC: 33762 AN: 41434

American (AMR) AF: 0.747 AC: 11406 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2831 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5090 AN: 5180

South Asian (SAS) AF: 0.816 AC: 3927 AN: 4814

European-Finnish (FIN) AF: 0.885 AC: 9371 AN: 10584

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57542 AN: 67986

Other (OTH) AF: 0.819 AC: 1723 AN: 2104

Alfa AF: 0.838 Hom.: 26992

Bravo AF: 0.821

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.099

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: rs4775919;

hg19: chr15-51445909;