11-82193215-A-G

Variant names:

• chr11-82193215-A-G
• rs1458949
• ENST00000500502.5:n.432-93008T>C

Variant summary

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

The ENST00000500502.5(MIR4300HG):​n.432-93008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,988 control chromosomes in the GnomAD database, including 13,670 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 0.42 (13670 hom., cov: 32)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500502.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	NR_120571.1		n.432-93008T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	ENST00000500502.5	TSL:1	n.432-93008T>C		intron	N/A
	MIR4300HG	ENST00000532217.1	TSL:5	n.558-93008T>C		intron	N/A
	MIR4300HG	ENST00000653173.1		n.185-93008T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63300 AN: 151870 Hom.: 13662 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.417 AC: 63326 AN: 151988 Hom.: 13670 Cov.: 32 AF XY: 0.414 AC XY: 30779 AN XY: 74294

African (AFR) AF: 0.325 AC: 13457 AN: 41430

American (AMR) AF: 0.351 AC: 5367 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2052 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1536 AN: 5160

South Asian (SAS) AF: 0.485 AC: 2336 AN: 4820

European-Finnish (FIN) AF: 0.441 AC: 4661 AN: 10558

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32488 AN: 67950

Other (OTH) AF: 0.414 AC: 875 AN: 2114

Alfa AF: 0.464 Hom.: 8755

Bravo AF: 0.404

Asia WGS AF: 0.376 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.4
DANN	Benign	0.75
PhyloP100		0.88

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1458949;

hg19: chr11-81904257;