rs892583

Positions:

• chr18-47390003-G-A
• chr18-47390003-G-C

Variant summary

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

The NR_147192.1(MIR4527HG):​n.38+104242G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,066 control chromosomes in the GnomAD database, including 45,925 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 0.77 (45925 hom., cov: 31)
• Consequence: MIR4527HG NR_147192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4527HG	NR_147192.1	n.38+104242G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+104242G>A		intron_variant, non_coding_transcript_variant		1
MIR4527HG	ENST00000598649.1	n.73+104206G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117621 AN: 151948 Hom.: 45877 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.774 AC: 117729 AN: 152066 Hom.: 45925 Cov.: 31 AF XY: 0.777 AC XY: 57722 AN XY: 74334

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.753

Alfa AF: 0.729 Hom.: 6583

Bravo AF: 0.771

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs892583; hg19: chr18-44916374;