rs1013273

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000653173.1	n.474+1415A>G		intron_variant	Intron 4 of 4
MIR4300HG	ENST00000659248.1	n.721+1415A>G		intron_variant	Intron 5 of 5

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.260

Alfa AF: 0.253 Hom.: 10376

Bravo AF: 0.247

Asia WGS AF: 0.341 AC: 1182 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013273; hg19: chr11-81534503;