chr13-87645970-G-T

Variant names:

• chr13-87645970-G-T
• rs9332444
• ENST00000436290.2:n.128+24866C>A

Variant summary

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

The ENST00000436290.2(MIR4500HG):​n.128+24866C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,850 control chromosomes in the GnomAD database, including 10,428 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 (10428 hom., cov: 32)
• Consequence: MIR4500HG ENST00000436290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900338	XM_047430855.1	c.*945+24866C>A		intron_variant	Intron 1 of 1		XP_047286811.1
MIR4500HG	NR_033829.1	n.128+24866C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4500HG	ENST00000436290.2	n.128+24866C>A		intron_variant	Intron 1 of 5	1
MIR4500HG	ENST00000441617.7	n.489+24866C>A		intron_variant	Intron 1 of 3	3
MIR4500HG	ENST00000453832.2	n.272-24812C>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52631 AN: 151732 Hom.: 10413 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.347 AC: 52684 AN: 151850 Hom.: 10428 Cov.: 32 AF XY: 0.360 AC XY: 26702 AN XY: 74204

African (AFR) AF: 0.311 AC: 12885 AN: 41410

American (AMR) AF: 0.362 AC: 5529 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1625 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4838 AN: 5146

South Asian (SAS) AF: 0.579 AC: 2777 AN: 4798

European-Finnish (FIN) AF: 0.390 AC: 4097 AN: 10512

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.292 AC: 19864 AN: 67938

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.306 Hom.: 987

Bravo AF: 0.344

Asia WGS AF: 0.726 AC: 2521 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.47
PhyloP100		-0.089

Splicing

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

Publications

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Other links and lift over

dbSNP: rs9332444; hg19: chr13-88298225;