rs4939797

Positions:

• chr18-47507115-G-A
• chr18-47507115-G-T

Variant summary

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

The NR_147192.1(MIR4527HG):​n.39-67481G>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 0.339 in 152,056 control chromosomes in the GnomAD database, including 9,760 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 0.34 (9760 hom., cov: 32)
• Consequence: MIR4527HG NR_147192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4527HG	NR_147192.1	n.39-67481G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000565127.1	n.69-4625G>A		intron_variant, non_coding_transcript_variant		4
MIR4527HG	ENST00000586905.3	n.38-67481G>A		intron_variant, non_coding_transcript_variant		1
MIR4527HG	ENST00000598649.1	n.74-54619G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51617 AN: 151938 Hom.: 9761 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.339 AC: 51612 AN: 152056 Hom.: 9760 Cov.: 32 AF XY: 0.332 AC XY: 24679 AN XY: 74330

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.0501

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.391

Alfa AF: 0.419 Hom.: 23930

Bravo AF: 0.334

Asia WGS AF: 0.174 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939797; hg19: chr18-45033486;