rs2186690

Variant names:

• chr11-82608305-A-G
• rs2186690
• ENST00000527364.2:n.485+1708T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527364.2(ENSG00000255246):​n.485+1708T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,158 control chromosomes in the GnomAD database, including 63,208 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 0.91 (63208 hom., cov: 33)
• Consequence: ENSG00000255246 ENST00000527364.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

ENSG00000255246 (HGNC:):

MIR4300HG (HGNC:52003): (MIR4300 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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
ENSG00000255246	ENST00000527364.2	n.485+1708T>C		intron_variant	Intron 4 of 4	3
MIR4300HG	ENST00000532217.1	n.440+64787T>C		intron_variant	Intron 3 of 4	5
ENSG00000255246	ENST00000661021.1	n.402-4204T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138497 AN: 152040 Hom.: 63138 Cov.: 33

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.911 AC: 138625 AN: 152158 Hom.: 63208 Cov.: 33 AF XY: 0.911 AC XY: 67792 AN XY: 74390

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.920

Alfa AF: 0.900 Hom.: 12571

Bravo AF: 0.914

Asia WGS AF: 0.921 AC: 3197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2186690; hg19: chr11-82319347;