11-82043646-C-T

Variant names:

• chr11-82043646-C-T
• rs678021
• ENST00000500502.5:n.814-27912G>A

Variant summary

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

The ENST00000500502.5(MIR4300HG):​n.814-27912G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 152,208 control chromosomes in the GnomAD database, including 689 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 0.085 (689 hom., cov: 32)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1	n.814-27912G>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.814-27912G>A		intron_variant	Intron 5 of 7	1
MIR4300HG	ENST00000530896.6	n.346-27912G>A		intron_variant	Intron 2 of 4	3
MIR4300HG	ENST00000653173.1	n.418+56328G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12857 AN: 152090 Hom.: 684 Cov.: 32

Gnomad AFR AF: 0.0297

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0846 AC: 12876 AN: 152208 Hom.: 689 Cov.: 32 AF XY: 0.0831 AC XY: 6185 AN XY: 74422

African (AFR) AF: 0.0296 AC: 1230 AN: 41530

American (AMR) AF: 0.145 AC: 2212 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0884 AC: 307 AN: 3472

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5178

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4826

European-Finnish (FIN) AF: 0.0758 AC: 804 AN: 10608

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7678 AN: 67996

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.106 Hom.: 154

Bravo AF: 0.0906

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.083
DANN	Benign	0.70
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs678021; hg19: chr11-81754688;