13-87644846-T-C

Variant names:

• chr13-87644846-T-C
• rs979969
• ENST00000436290.2:n.128+25990A>G

Variant summary

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

The ENST00000436290.2(MIR4500HG):​n.128+25990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,590 control chromosomes in the GnomAD database, including 20,405 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 0.50 (20405 hom., cov: 30)
• Consequence: MIR4500HG ENST00000436290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 4 publications found

Genes affected

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

LOC124900338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436290.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4500HG	NR_033829.1		n.128+25990A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4500HG	ENST00000436290.2	TSL:1	n.128+25990A>G		intron	N/A
	MIR4500HG	ENST00000441617.7	TSL:3	n.489+25990A>G		intron	N/A
	MIR4500HG	ENST00000453832.2	TSL:3	n.272-23688A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75486 AN: 151472 Hom.: 20362 Cov.: 30

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.499 AC: 75581 AN: 151590 Hom.: 20405 Cov.: 30 AF XY: 0.509 AC XY: 37671 AN XY: 74050

African (AFR) AF: 0.646 AC: 26719 AN: 41356

American (AMR) AF: 0.451 AC: 6862 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1730 AN: 3466

East Asian (EAS) AF: 0.944 AC: 4858 AN: 5146

South Asian (SAS) AF: 0.633 AC: 3045 AN: 4810

European-Finnish (FIN) AF: 0.516 AC: 5393 AN: 10452

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25549 AN: 67854

Other (OTH) AF: 0.484 AC: 1016 AN: 2100

Alfa AF: 0.400 Hom.: 9415

Bravo AF: 0.500

Asia WGS AF: 0.779 AC: 2697 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-0.78

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs979969;

hg19: chr13-88297101;