rs869817

Variant names:

• chr2-11876873-C-T
• rs869817
• ENST00000438292.5:n.31+10958C>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000438292.5	n.31+10958C>T		intron_variant	Intron 1 of 4	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;