chr11-82193215-A-G

Position:

• chr11-82193215-A-G

Variant summary

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

The NR_120571.1(MIR4300HG):​n.432-93008T>C variant causes a intron, non coding transcript 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 NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4300HG	NR_120571.1	n.432-93008T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.558-93008T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.414

Alfa AF: 0.464 Hom.: 7833

Bravo AF: 0.404

Asia WGS AF: 0.376 AC: 1312 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	8.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458949; hg19: chr11-81904257;