rs17546105

chr2-11891415-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3681HG	ENST00000438292.5	n.31+25500T>C		intron_variant, non_coding_transcript_variant		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;