rs1594887

Positions:

• chr18-47365998-G-A

Variant summary

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

The NR_147192.1(MIR4527HG):​n.38+80237G>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 0.738 in 152,114 control chromosomes in the GnomAD database, including 41,554 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 (41554 hom., cov: 32)
• Consequence: MIR4527HG NR_147192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

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=-1.0).
• 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/exons	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.38+80237G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+80237G>A		intron_variant, non_coding_transcript_variant		1
MIR4527HG	ENST00000598649.1	n.73+80201G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112156 AN: 151996 Hom.: 41507 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.738 AC: 112261 AN: 152114 Hom.: 41554 Cov.: 32 AF XY: 0.743 AC XY: 55242 AN XY: 74392

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.726

Alfa AF: 0.727 Hom.: 66126

Bravo AF: 0.728

Asia WGS AF: 0.816 AC: 2839 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	0.12
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1594887; hg19: chr18-44892369;