rs869817

chr2-11876873-C-T

Variant summary

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

The ENST00000438292.5(MIR3681HG):n.31+10958C>T 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 0.375 in 152,028 control chromosomes in the GnomAD database, including 12,715 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 0.38 (12715 hom., cov: 32)
• Consequence: MIR3681HG ENST00000438292.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 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+10958C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56961 AN: 151910 Hom.: 12680 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.375 AC: 57062 AN: 152028 Hom.: 12715 Cov.: 32 AF XY: 0.371 AC XY: 27591 AN XY: 74314

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0509

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.347

Alfa AF: 0.306 Hom.: 4814

Bravo AF: 0.384

Asia WGS AF: 0.183 AC: 641 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	0.19
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs869817; hg19: chr2-12016999;