rs10929808

chr2-12428870-G-A

Variant summary

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

The NR_110196.1(MIR3681HG):n.424+120086G>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 0.86 in 152,236 control chromosomes in the GnomAD database, including 56,690 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 0.86 (56690 hom., cov: 33)
• Consequence: MIR3681HG NR_110196.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3681HG	NR_110196.1	n.424+120086G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3681HG	ENST00000412294.5	n.412+120086G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130725 AN: 152118 Hom.: 56634 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.860 AC: 130849 AN: 152236 Hom.: 56690 Cov.: 33 AF XY: 0.852 AC XY: 63422 AN XY: 74428

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.870

Alfa AF: 0.863 Hom.: 122981

Bravo AF: 0.859

Asia WGS AF: 0.601 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10929808; hg19: chr2-12568996;