rs1534422

Positions:

• chr2-12500615-G-A
• chr2-12500615-G-T

Variant summary

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

The ENST00000412294.5(MIR3681HG):​n.413-57591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,908 control chromosomes in the GnomAD database, including 20,978 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 0.52 (20978 hom., cov: 31)
• Consequence: MIR3681HG ENST00000412294.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

MIR3681HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3681HG	NR_110196.1	n.425-57591G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000412294.5	n.413-57591G>A		intron_variant		2
MIR3681HG	ENST00000412606.2	n.86-57591G>A		intron_variant		5
MIR3681HG	ENST00000653212.1	n.438-57591G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79142 AN: 151790 Hom.: 20965 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.521 AC: 79187 AN: 151908 Hom.: 20978 Cov.: 31 AF XY: 0.525 AC XY: 38979 AN XY: 74228

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.546

Alfa AF: 0.536 Hom.: 31452

Bravo AF: 0.515

Asia WGS AF: 0.587 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1534422; hg19: chr2-12640741;