rs11694463

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 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	ENST00000664018.1	n.579-32734T>C		intron_variant	Intron 4 of 5

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.0933

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.127

Alfa AF: 0.109 Hom.: 544

Bravo AF: 0.113

Asia WGS AF: 0.129 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11694463; hg19: chr2-12781621;