rs1529806

Variant names:

• chr18-47376622-G-A
• rs1529806
• ENST00000586905.3:n.37+90861G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-47376622-G-A
• chr18-47376622-G-T

Variant summary

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

The ENST00000586905.3(MIR4527HG):​n.37+90861G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,068 control chromosomes in the GnomAD database, including 41,251 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 0.74 (41251 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.38+90861G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+90861G>A		intron_variant	Intron 1 of 2	1
MIR4527HG	ENST00000598649.1	n.73+90825G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111713 AN: 151950 Hom.: 41203 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.735 AC: 111820 AN: 152068 Hom.: 41251 Cov.: 32 AF XY: 0.740 AC XY: 54995 AN XY: 74324

African (AFR) AF: 0.726 AC: 30090 AN: 41460

American (AMR) AF: 0.678 AC: 10368 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2655 AN: 3468

East Asian (EAS) AF: 0.886 AC: 4571 AN: 5160

South Asian (SAS) AF: 0.787 AC: 3788 AN: 4814

European-Finnish (FIN) AF: 0.828 AC: 8762 AN: 10576

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.722 AC: 49080 AN: 67984

Other (OTH) AF: 0.722 AC: 1527 AN: 2114

Alfa AF: 0.730 Hom.: 29103

Bravo AF: 0.725

Asia WGS AF: 0.815 AC: 2838 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	0.076
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1529806; hg19: chr18-44902993;