rs662334

Variant names:

• chr11-82265293-A-G
• rs662334
• ENST00000500502.5:n.431+84633T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-82265293-A-G
• chr11-82265293-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500502.5(MIR4300HG):​n.431+84633T>C variant causes a intron 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 ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 1 publications found

Genes affected

MIR4300HG (HGNC:52003): (MIR4300 host gene)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1	n.431+84633T>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.431+84633T>C		intron_variant	Intron 3 of 7	1
MIR4300HG	ENST00000532217.1	n.557+91219T>C		intron_variant	Intron 4 of 4	5
MIR4300HG	ENST00000653173.1	n.184+91219T>C		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.816 AC: 33836 AN: 41478

American (AMR) AF: 0.686 AC: 10448 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2694 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4026 AN: 5154

South Asian (SAS) AF: 0.727 AC: 3499 AN: 4814

European-Finnish (FIN) AF: 0.606 AC: 6378 AN: 10520

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.647 AC: 43842 AN: 67802

Other (OTH) AF: 0.694 AC: 1461 AN: 2106

Alfa AF: 0.561 Hom.: 1812

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs662334; hg19: chr11-81976335;