rs35451359

Variant names:

• chr18-47584609-C-CTCTA
• rs35451359
• ENST00000586905.3:n.174-9440_174-9439insTCTA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000586905.3(MIR4527HG):​n.174-9440_174-9439insTCTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0966 in 152,104 control chromosomes in the GnomAD database, including 1,927 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.097 (1927 hom., cov: 31)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 2 publications found

Genes affected

MIR4527HG (HGNC:31724): (MIR4527 host gene)

ENSG00000301225 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586905.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	NR_147192.1		n.175-9437_175-9436insATCT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.174-9440_174-9439insTCTA		intron	N/A
	MIR4527HG	ENST00000600127.1	TSL:5	n.615+1816_615+1817insTCTA		intron	N/A
	ENSG00000301225	ENST00000777134.1		n.244+6661_244+6662insTAGA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0963 AC: 14642 AN: 151986 Hom.: 1910 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0966 AC: 14697 AN: 152104 Hom.: 1927 Cov.: 31 AF XY: 0.0926 AC XY: 6886 AN XY: 74392

African (AFR) AF: 0.302 AC: 12514 AN: 41400

American (AMR) AF: 0.0396 AC: 605 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00872 AC: 42 AN: 4818

European-Finnish (FIN) AF: 0.0129 AC: 137 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1209 AN: 68016

Other (OTH) AF: 0.0719 AC: 152 AN: 2114

Alfa AF: 0.0659 Hom.: 133

Bravo AF: 0.109

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs35451359; hg19: chr18-45110980;