chr18-47530300-G-A

Position:

• chr18-47530300-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.39-44296G>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 0.181 in 152,160 control chromosomes in the GnomAD database, including 2,650 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 0.18 (2650 hom., cov: 33)
• Consequence: MIR4527HG NR_147192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.78

Genes affected

(HGNC:):

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.39-44296G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000565127.1	n.276-15114G>A		intron_variant, non_coding_transcript_variant		4
MIR4527HG	ENST00000586905.3	n.38-44296G>A		intron_variant, non_coding_transcript_variant		1
MIR4527HG	ENST00000598649.1	n.74-31434G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27483 AN: 152042 Hom.: 2645 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.181 AC: 27501 AN: 152160 Hom.: 2650 Cov.: 33 AF XY: 0.183 AC XY: 13619 AN XY: 74386

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.151

Alfa AF: 0.168 Hom.: 1150

Bravo AF: 0.171

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	16
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6507763; hg19: chr18-45056671;