rs2016354

Variant names:

• chr8-74647264-C-T
• rs2016354
• ENST00000518190.4:n.379+21923C>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+21923C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,010 control chromosomes in the GnomAD database, including 13,441 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 0.40 (13441 hom., cov: 32)
• Consequence: MIR2052HG ENST00000518190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR2052HG	NR_033830.1	n.131+34324C>T		intron_variant	Intron 2 of 5
MIR2052HG	NR_197229.1	n.240+34324C>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+21923C>T		intron_variant	Intron 4 of 5	4
MIR2052HG	ENST00000523118.5	n.131+34324C>T		intron_variant	Intron 2 of 5	2
MIR2052HG	ENST00000523442.5	n.216+34324C>T		intron_variant	Intron 2 of 6	4

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61118 AN: 151892 Hom.: 13444 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.402 AC: 61116 AN: 152010 Hom.: 13441 Cov.: 32 AF XY: 0.397 AC XY: 29469 AN XY: 74276

African (AFR) AF: 0.232 AC: 9639 AN: 41482

American (AMR) AF: 0.427 AC: 6515 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1813 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3432 AN: 5174

South Asian (SAS) AF: 0.383 AC: 1843 AN: 4814

European-Finnish (FIN) AF: 0.348 AC: 3675 AN: 10548

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32674 AN: 67944

Other (OTH) AF: 0.453 AC: 954 AN: 2106

Alfa AF: 0.457 Hom.: 8642

Bravo AF: 0.405

Asia WGS AF: 0.471 AC: 1637 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.68
PhyloP100		-0.94
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: rs2016354; hg19: chr8-75559499;