chr13-87476206-G-C

Variant names:

• chr13-87476206-G-C
• rs1417497
• ENST00000436290.2:n.234-2653C>G

Variant summary

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

The ENST00000436290.2(MIR4500HG):​n.234-2653C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 151,836 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 0.078 (517 hom., cov: 32)
• Consequence: MIR4500HG ENST00000436290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 1 publications found

Genes affected

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

ENSG00000285699 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4500HG	NR_033829.1	n.234-2653C>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4500HG	ENST00000436290.2	n.234-2653C>G		intron_variant	Intron 2 of 5	1
MIR4500HG	ENST00000717729.1	n.300+1160C>G		intron_variant	Intron 2 of 8
MIR4500HG	ENST00000717730.1	n.1095-2653C>G		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11876 AN: 151718 Hom.: 518 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0783 AC: 11882 AN: 151836 Hom.: 517 Cov.: 32 AF XY: 0.0751 AC XY: 5570 AN XY: 74186

African (AFR) AF: 0.114 AC: 4736 AN: 41486

American (AMR) AF: 0.0593 AC: 903 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3468

East Asian (EAS) AF: 0.0149 AC: 77 AN: 5168

South Asian (SAS) AF: 0.0385 AC: 186 AN: 4828

European-Finnish (FIN) AF: 0.0532 AC: 561 AN: 10544

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0699 AC: 4738 AN: 67800

Other (OTH) AF: 0.0862 AC: 181 AN: 2100

Alfa AF: 0.0291 Hom.: 14

Bravo AF: 0.0797

Asia WGS AF: 0.0380 AC: 130 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1417497; hg19: chr13-88128461;