rs2033877

Positions:

• chr2-11955762-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000438292.5	n.32-51985G>A		intron_variant, non_coding_transcript_variant		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;