18-47409375-T-G

Variant names:

• chr18-47409375-T-G
• rs9807521
• ENST00000586905.3:n.37+123614T>G

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.37+123614T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,186 control chromosomes in the GnomAD database, including 47,345 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 0.79 (47345 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.38+123614T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+123614T>G		intron_variant	Intron 1 of 2	1
MIR4527HG	ENST00000598649.1	n.73+123578T>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119362 AN: 152068 Hom.: 47282 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.785 AC: 119486 AN: 152186 Hom.: 47345 Cov.: 32 AF XY: 0.788 AC XY: 58642 AN XY: 74398

African (AFR) AF: 0.875 AC: 36350 AN: 41526

American (AMR) AF: 0.776 AC: 11872 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2623 AN: 3470

East Asian (EAS) AF: 0.935 AC: 4840 AN: 5178

South Asian (SAS) AF: 0.791 AC: 3815 AN: 4824

European-Finnish (FIN) AF: 0.808 AC: 8553 AN: 10590

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48907 AN: 67980

Other (OTH) AF: 0.761 AC: 1608 AN: 2114

Alfa AF: 0.739 Hom.: 51017

Bravo AF: 0.792

Asia WGS AF: 0.843 AC: 2934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.51
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs9807521; hg19: chr18-44935746;