18-47403287-T-C

Variant names:

• chr18-47403287-T-C
• rs977160
• ENST00000586905.3:n.37+117526T>C

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.37+117526T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,132 control chromosomes in the GnomAD database, including 43,570 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 0.76 (43570 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

MIR4527HG (HGNC:31724): (MIR4527 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 (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.38+117526T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+117526T>C		intron_variant	Intron 1 of 2	1
MIR4527HG	ENST00000598649.1	n.73+117490T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114829 AN: 152014 Hom.: 43519 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.756 AC: 114941 AN: 152132 Hom.: 43570 Cov.: 32 AF XY: 0.760 AC XY: 56525 AN XY: 74368

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.753

Alfa AF: 0.666 Hom.: 2205

Bravo AF: 0.755

Asia WGS AF: 0.836 AC: 2909 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	0.19
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977160; hg19: chr18-44929658;