rs4027132

Variant names:

• chr2-11897366-G-A
• rs4027132
• ENST00000438292.5:n.31+31451G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-11897366-G-A
• chr2-11897366-G-C
• chr2-11897366-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438292.5(MIR3681HG):​n.31+31451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 150,690 control chromosomes in the GnomAD database, including 25,137 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 0.58 (25137 hom., cov: 30)
• Consequence: MIR3681HG ENST00000438292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 15 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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+31451G>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.577 AC: 86898 AN: 150586 Hom.: 25106 Cov.: 30

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.577 AC: 86973 AN: 150690 Hom.: 25137 Cov.: 30 AF XY: 0.583 AC XY: 42801 AN XY: 73436

African (AFR) AF: 0.609 AC: 24994 AN: 41068

American (AMR) AF: 0.594 AC: 8959 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2221 AN: 5102

South Asian (SAS) AF: 0.569 AC: 2688 AN: 4720

European-Finnish (FIN) AF: 0.674 AC: 6883 AN: 10218

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37419 AN: 67760

Other (OTH) AF: 0.570 AC: 1184 AN: 2078

Alfa AF: 0.551 Hom.: 100094

Bravo AF: 0.567

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs4027132; hg19: chr2-12037492;