rs2033877

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438292.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000438292.5	TSL:3	n.32-51985G>A		intron	N/A

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

African (AFR) AF: 0.380 AC: 15727 AN: 41386

American (AMR) AF: 0.262 AC: 4009 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 848 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1581 AN: 5144

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4808

European-Finnish (FIN) AF: 0.228 AC: 2403 AN: 10562

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19439 AN: 67952

Other (OTH) AF: 0.274 AC: 579 AN: 2116

Alfa AF: 0.291 Hom.: 5176

Bravo AF: 0.312

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.83
PhyloP100		-0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2033877;

hg19: chr2-12095888;