rs662334

chr11-82265293-A-Gchr11-82265293-A-T

Variant summary

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

The NR_120571.1(MIR4300HG):n.431+84633T>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 0.705 in 151,776 control chromosomes in the GnomAD database, including 38,168 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 0.70 (38168 hom., cov: 31)
• Consequence: MIR4300HG NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4300HG	NR_120571.1	n.431+84633T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.557+91219T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106861 AN: 151660 Hom.: 38127 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.705 AC: 106953 AN: 151776 Hom.: 38168 Cov.: 31 AF XY: 0.705 AC XY: 52286 AN XY: 74122

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.694

Alfa AF: 0.535 Hom.: 1520

Bravo AF: 0.714

Asia WGS AF: 0.734 AC: 2539 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs662334; hg19: chr11-81976335;