rs17546105

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.7).
• 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

African (AFR) AF: 0.0254 AC: 1051 AN: 41394

American (AMR) AF: 0.0546 AC: 832 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5170

South Asian (SAS) AF: 0.0529 AC: 254 AN: 4806

European-Finnish (FIN) AF: 0.0884 AC: 920 AN: 10404

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0819 AC: 5560 AN: 67920

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0768 Hom.: 928

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
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs17546105; hg19: chr2-12031541;