13-87577000-C-G

Variant names:

• chr13-87577000-C-G
• rs9300547
• ENST00000436290.2:n.129-65530G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000436290.2(MIR4500HG):​n.129-65530G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,798 control chromosomes in the GnomAD database, including 9,995 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 0.35 (9995 hom., cov: 32)
• Consequence: MIR4500HG ENST00000436290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 1 publications found

Genes affected

MIR4500HG (HGNC:42773): (MIR4500 host gene)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4500HG	NR_033829.1	n.129-65530G>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4500HG	ENST00000436290.2	n.129-65530G>C		intron_variant	Intron 1 of 5	1
MIR4500HG	ENST00000656150.1	n.656-16583G>C		intron_variant	Intron 2 of 4
MIR4500HG	ENST00000658487.2	n.687+38563G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53797 AN: 151680 Hom.: 9984 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.355 AC: 53837 AN: 151798 Hom.: 9995 Cov.: 32 AF XY: 0.359 AC XY: 26663 AN XY: 74182

African (AFR) AF: 0.267 AC: 11053 AN: 41392

American (AMR) AF: 0.467 AC: 7113 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3468

East Asian (EAS) AF: 0.442 AC: 2277 AN: 5148

South Asian (SAS) AF: 0.389 AC: 1876 AN: 4826

European-Finnish (FIN) AF: 0.415 AC: 4373 AN: 10534

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24676 AN: 67890

Other (OTH) AF: 0.365 AC: 770 AN: 2108

Alfa AF: 0.373 Hom.: 1351

Bravo AF: 0.353

Asia WGS AF: 0.433 AC: 1502 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.74
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs9300547; hg19: chr13-88229255;