rs953291

Variant names:

• chr18-47344128-T-C
• rs953291
• ENST00000586905.3:n.37+58367T>C

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.37+58367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,146 control chromosomes in the GnomAD database, including 8,603 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 (8603 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 2 publications found

Genes affected

MIR4527HG (HGNC:31724): (MIR4527 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586905.3. 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
	MIR4527HG	NR_147192.1		n.38+58367T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.37+58367T>C		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.73+58331T>C		intron	N/A
	MIR4527HG	ENST00000833748.1		n.409-14169T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47681 AN: 152028 Hom.: 8607 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.313 AC: 47672 AN: 152146 Hom.: 8603 Cov.: 32 AF XY: 0.315 AC XY: 23403 AN XY: 74382

African (AFR) AF: 0.123 AC: 5095 AN: 41538

American (AMR) AF: 0.358 AC: 5470 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1468 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5166

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4816

European-Finnish (FIN) AF: 0.428 AC: 4528 AN: 10580

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26494 AN: 67976

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.330 Hom.: 1116

Bravo AF: 0.305

Asia WGS AF: 0.276 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.85
PhyloP100		-0.17

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: rs953291;

hg19: chr18-44870499;