rs605335

chr11-82201688-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.432-101481T>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 0.361 in 151,900 control chromosomes in the GnomAD database, including 10,424 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 0.36 (10424 hom., cov: 31)
• Consequence: MIR4300HG NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4300HG	NR_120571.1	n.432-101481T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.558-101481T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54694 AN: 151782 Hom.: 10401 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.361 AC: 54772 AN: 151900 Hom.: 10424 Cov.: 31 AF XY: 0.362 AC XY: 26869 AN XY: 74232

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.356

Alfa AF: 0.327 Hom.: 1066

Bravo AF: 0.376

Asia WGS AF: 0.382 AC: 1326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.7
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs605335; hg19: chr11-81912730;