rs2033877

Variant names:

• chr2-11955762-G-A
• rs2033877
• ENST00000438292.5:n.32-51985G>A

Variant summary

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

The ENST00000438292.5(MIR3681HG):​n.32-51985G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,912 control chromosomes in the GnomAD database, including 7,319 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 0.31 (7319 hom., cov: 31)
• Consequence: MIR3681HG ENST00000438292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

Genes affected

MIR3681HG (HGNC:52001): (MIR3681 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000438292.5	n.32-51985G>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46348 AN: 151794 Hom.: 7296 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.306 AC: 46411 AN: 151912 Hom.: 7319 Cov.: 31 AF XY: 0.301 AC XY: 22314 AN XY: 74238

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.274

Alfa AF: 0.291 Hom.: 3930

Bravo AF: 0.312

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2033877; hg19: chr2-12095888;