rs1013273

Variant names:

• chr11-81823461-T-C
• rs1013273
• ENST00000653173.1:n.474+1415A>G

Variant summary

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

The ENST00000653173.1(MIR4300HG):​n.474+1415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,146 control chromosomes in the GnomAD database, including 4,946 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 0.25 (4946 hom., cov: 33)
• Consequence: MIR4300HG ENST00000653173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 7 publications found

Genes affected

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

ENSG00000295219 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653173.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	ENST00000653173.1		n.474+1415A>G		intron	N/A
	MIR4300HG	ENST00000659248.1		n.721+1415A>G		intron	N/A
	ENSG00000295219	ENST00000728683.1		n.205-2018T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37904 AN: 152028 Hom.: 4937 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.249 AC: 37948 AN: 152146 Hom.: 4946 Cov.: 33 AF XY: 0.250 AC XY: 18619 AN XY: 74382

African (AFR) AF: 0.261 AC: 10849 AN: 41530

American (AMR) AF: 0.224 AC: 3427 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1046 AN: 3472

East Asian (EAS) AF: 0.180 AC: 930 AN: 5176

South Asian (SAS) AF: 0.485 AC: 2337 AN: 4822

European-Finnish (FIN) AF: 0.191 AC: 2019 AN: 10592

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16573 AN: 67964

Other (OTH) AF: 0.260 AC: 550 AN: 2116

Alfa AF: 0.251 Hom.: 15597

Bravo AF: 0.247

Asia WGS AF: 0.341 AC: 1182 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.85
PhyloP100		0.0030

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: rs1013273;

hg19: chr11-81534503;