rs6472866

Variant names:

• chr8-74600899-C-T
• rs6472866
• ENST00000518190.4:n.134+991C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518190.4(MIR2052HG):​n.134+991C>T variant causes a intron 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 ENST00000518190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 8 publications found

Genes affected

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

LINC03071 (HGNC:56645): (long intergenic non-protein coding RNA 3071)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR2052HG	NR_033830.1	n.43+991C>T		intron_variant	Intron 1 of 5
MIR2052HG	NR_197229.1	n.152+991C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR2052HG	ENST00000518190.4	n.134+991C>T		intron_variant	Intron 1 of 5	4
MIR2052HG	ENST00000523118.5	n.43+991C>T		intron_variant	Intron 1 of 5	2
MIR2052HG	ENST00000523442.5	n.128+991C>T		intron_variant	Intron 1 of 6	4

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

African (AFR) AF: 0.491 AC: 20350 AN: 41432

American (AMR) AF: 0.446 AC: 6818 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1792 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3453 AN: 5134

South Asian (SAS) AF: 0.395 AC: 1896 AN: 4806

European-Finnish (FIN) AF: 0.329 AC: 3479 AN: 10568

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27329 AN: 67948

Other (OTH) AF: 0.445 AC: 939 AN: 2108

Alfa AF: 0.429 Hom.: 47577

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
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6472866; hg19: chr8-75513134;