2-12641495-T-C

Variant names:

• chr2-12641495-T-C
• rs11694463
• ENST00000664018.1:n.579-32734T>C

Variant summary

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

The ENST00000664018.1(MIR3681HG):​n.579-32734T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,264 control chromosomes in the GnomAD database, including 979 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 0.11 (979 hom., cov: 33)
• Consequence: MIR3681HG ENST00000664018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 1 publications found

Genes affected

MIR3681HG (HGNC:52001): (MIR3681 host gene)

ENSG00000309353 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664018.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000664018.1		n.579-32734T>C		intron	N/A
	MIR3681HG	ENST00000840289.1		n.240-32734T>C		intron	N/A
	MIR3681HG	ENST00000840290.1		n.235-32734T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17066 AN: 152146 Hom.: 979 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.0933

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.112 AC: 17074 AN: 152264 Hom.: 979 Cov.: 33 AF XY: 0.112 AC XY: 8325 AN XY: 74452

African (AFR) AF: 0.125 AC: 5191 AN: 41538

American (AMR) AF: 0.0924 AC: 1413 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0933 AC: 324 AN: 3472

East Asian (EAS) AF: 0.152 AC: 789 AN: 5180

South Asian (SAS) AF: 0.139 AC: 671 AN: 4828

European-Finnish (FIN) AF: 0.0848 AC: 900 AN: 10614

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7386 AN: 68012

Other (OTH) AF: 0.127 AC: 269 AN: 2116

Alfa AF: 0.109 Hom.: 725

Bravo AF: 0.113

Asia WGS AF: 0.129 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.66
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11694463; hg19: chr2-12781621;