rs676413

Variant names:

• chr11-82188594-T-A
• rs676413
• ENST00000500502.5:n.432-88387A>T

Variant summary

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

The ENST00000500502.5(MIR4300HG):​n.432-88387A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,294 control chromosomes in the GnomAD database, including 517 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 0.074 (517 hom., cov: 33)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1	n.432-88387A>T		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.432-88387A>T		intron_variant	Intron 3 of 7	1
MIR4300HG	ENST00000532217.1	n.558-88387A>T		intron_variant	Intron 4 of 4	5
MIR4300HG	ENST00000653173.1	n.185-88387A>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11202 AN: 152176 Hom.: 514 Cov.: 33

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0736 AC: 11214 AN: 152294 Hom.: 517 Cov.: 33 AF XY: 0.0724 AC XY: 5393 AN XY: 74462

African (AFR) AF: 0.0206 AC: 857 AN: 41564

American (AMR) AF: 0.104 AC: 1587 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5182

South Asian (SAS) AF: 0.0408 AC: 197 AN: 4828

European-Finnish (FIN) AF: 0.0567 AC: 602 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7292 AN: 68010

Other (OTH) AF: 0.0926 AC: 196 AN: 2116

Alfa AF: 0.0902 Hom.: 84

Bravo AF: 0.0759

Asia WGS AF: 0.0270 AC: 94 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs676413; hg19: chr11-81899636;