8-74640865-C-T

Variant names:

• chr8-74640865-C-T
• rs1365032
• ENST00000518190.4:n.379+15524C>T

Variant summary

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

The ENST00000518190.4(MIR2052HG):​n.379+15524C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,980 control chromosomes in the GnomAD database, including 15,398 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 (15398 hom., cov: 33)
• Consequence: MIR2052HG ENST00000518190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR2052HG	NR_033830.1	n.131+27925C>T		intron_variant	Intron 2 of 5
MIR2052HG	NR_197229.1	n.240+27925C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR2052HG	ENST00000518190.4	n.379+15524C>T		intron_variant	Intron 4 of 5	4
MIR2052HG	ENST00000523118.5	n.131+27925C>T		intron_variant	Intron 2 of 5	2
MIR2052HG	ENST00000523442.5	n.216+27925C>T		intron_variant	Intron 2 of 6	4

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67368 AN: 151860 Hom.: 15394 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.443 AC: 67396 AN: 151980 Hom.: 15398 Cov.: 33 AF XY: 0.436 AC XY: 32364 AN XY: 74268

African (AFR) AF: 0.368 AC: 15243 AN: 41452

American (AMR) AF: 0.449 AC: 6862 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3402 AN: 5122

South Asian (SAS) AF: 0.383 AC: 1847 AN: 4824

European-Finnish (FIN) AF: 0.347 AC: 3667 AN: 10558

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32848 AN: 67974

Other (OTH) AF: 0.498 AC: 1049 AN: 2106

Alfa AF: 0.478 Hom.: 35234

Bravo AF: 0.453

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.3
DANN	Benign	0.54
PhyloP100		-0.81
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: rs1365032; hg19: chr8-75553100;