rs2186690

Positions:

• chr11-82608305-A-G

Variant summary

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

The ENST00000532217.1(MIR4300HG):​n.440+64787T>C variant causes a intron, non coding transcript 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: MIR4300HG ENST00000532217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

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

(HGNC:):

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.440+64787T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000661021.1	n.402-4204T>C		intron_variant, non_coding_transcript_variant
	ENST00000527364.2	n.485+1708T>C		intron_variant, non_coding_transcript_variant		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;