11-81871697-T-C

Variant names:

• chr11-81871697-T-C
• rs1459952
• ENST00000653173.1:n.419-46766A>G

Variant summary

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

The ENST00000653173.1(MIR4300HG):​n.419-46766A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 151,678 control chromosomes in the GnomAD database, including 46,179 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 0.77 (46179 hom., cov: 31)
• Consequence: MIR4300HG ENST00000653173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 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.419-46766A>G		intron_variant	Intron 3 of 4
MIR4300HG	ENST00000659248.1	n.666-46766A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117291 AN: 151562 Hom.: 46131 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.774 AC: 117398 AN: 151678 Hom.: 46179 Cov.: 31 AF XY: 0.769 AC XY: 57004 AN XY: 74086

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.750

Alfa AF: 0.752 Hom.: 10598

Bravo AF: 0.775

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1459952; hg19: chr11-81582739;