ENST00000438292.5:n.31+25500T>C

Variant names:

• chr2-11891415-T-C
• rs17546105
• ENST00000438292.5:n.31+25500T>C

Variant summary

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

The ENST00000438292.5(MIR3681HG):​n.31+25500T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 151,716 control chromosomes in the GnomAD database, including 336 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 0.061 (336 hom., cov: 31)
• Consequence: MIR3681HG ENST00000438292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

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=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0801 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.31+25500T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0613 AC: 9290 AN: 151614 Hom.: 335 Cov.: 31

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0523

Gnomad FIN AF: 0.0884

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0612 AC: 9289 AN: 151716 Hom.: 336 Cov.: 31 AF XY: 0.0605 AC XY: 4486 AN XY: 74098

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0529

Gnomad4 FIN AF: 0.0884

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0799 Hom.: 704

Bravo AF: 0.0571

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17546105; hg19: chr2-12031541;