18-47392956-T-C

Position:

• chr18-47392956-T-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+107195T>C 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 0.263 in 152,034 control chromosomes in the GnomAD database, including 6,044 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 0.26 (6044 hom., cov: 32)
• Consequence: MIR4527HG NR_147192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4527HG	NR_147192.1	n.38+107195T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+107195T>C		intron_variant, non_coding_transcript_variant		1
MIR4527HG	ENST00000598649.1	n.73+107159T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40027 AN: 151918 Hom.: 6044 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.263 AC: 40026 AN: 152034 Hom.: 6044 Cov.: 32 AF XY: 0.267 AC XY: 19820 AN XY: 74306

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.296

Alfa AF: 0.236 Hom.: 1020

Bravo AF: 0.256

Asia WGS AF: 0.266 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.84
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893784; hg19: chr18-44919327;