rs6472866

chr8-74600899-C-T

Variant summary

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

The NR_033830.1(MIR2052HG):n.43+991C>T 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 0.438 in 151,950 control chromosomes in the GnomAD database, including 14,903 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 0.44 (14903 hom., cov: 32)
• Consequence: MIR2052HG NR_033830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

Genes affected

MIR2052HG (HGNC:51555): (MIR2052 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR2052HG	NR_033830.1	n.43+991C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR2052HG	ENST00000523442.5	n.128+991C>T		intron_variant, non_coding_transcript_variant		4
MIR2052HG	ENST00000518190.4	n.134+991C>T		intron_variant, non_coding_transcript_variant		4
MIR2052HG	ENST00000523118.5	n.43+991C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66461 AN: 151832 Hom.: 14891 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.438 AC: 66502 AN: 151950 Hom.: 14903 Cov.: 32 AF XY: 0.436 AC XY: 32347 AN XY: 74256

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.445

Alfa AF: 0.431 Hom.: 20014

Bravo AF: 0.453

Asia WGS AF: 0.533 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6472866; hg19: chr8-75513134;