11-82064908-T-G

Variant names:

• chr11-82064908-T-G
• rs2851687
• ENST00000500502.5:n.813+31553A>C

Variant summary

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

The ENST00000500502.5(MIR4300HG):​n.813+31553A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.089 in 152,116 control chromosomes in the GnomAD database, including 725 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 0.089 (725 hom., cov: 32)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

Genes affected

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1	n.813+31553A>C		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.813+31553A>C		intron_variant	Intron 5 of 7	1
MIR4300HG	ENST00000530896.6	n.345+35066A>C		intron_variant	Intron 2 of 4	3
MIR4300HG	ENST00000653173.1	n.418+35066A>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 13489 AN: 151998 Hom.: 717 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0890 AC: 13531 AN: 152116 Hom.: 725 Cov.: 32 AF XY: 0.0875 AC XY: 6511 AN XY: 74376

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0629 Hom.: 97

Bravo AF: 0.0951

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851687; hg19: chr11-81775950;