2-12291314-T-C

Variant names:

• chr2-12291314-T-C
• rs723504
• ENST00000412294.6:n.326-17374T>C

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.326-17374T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,070 control chromosomes in the GnomAD database, including 23,158 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 (23158 hom., cov: 32)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412294.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	NR_110196.1		n.328-17374T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000412294.6	TSL:2	n.326-17374T>C		intron	N/A
	MIR3681HG	ENST00000438292.5	TSL:3	n.247-17374T>C		intron	N/A
	MIR3681HG	ENST00000653212.1		n.142+13441T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79667 AN: 151952 Hom.: 23142 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.524 AC: 79700 AN: 152070 Hom.: 23158 Cov.: 32 AF XY: 0.530 AC XY: 39377 AN XY: 74336

African (AFR) AF: 0.258 AC: 10695 AN: 41504

American (AMR) AF: 0.544 AC: 8304 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2163 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4095 AN: 5172

South Asian (SAS) AF: 0.651 AC: 3126 AN: 4800

European-Finnish (FIN) AF: 0.671 AC: 7100 AN: 10574

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42280 AN: 67966

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.587 Hom.: 91463

Bravo AF: 0.503

Asia WGS AF: 0.690 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.71
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs723504; hg19: chr2-12431440;