13-87644846-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047430855.1(LOC124900338):​c.*945+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: LOC124900338 XM_047430855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775

Genes affected

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

LOC124900338 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900338	XM_047430855.1	c.*945+25990A>G		intron_variant	Intron 1 of 1		XP_047286811.1
MIR4500HG	NR_033829.1	n.128+25990A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4500HG	ENST00000436290.2	n.128+25990A>G		intron_variant	Intron 1 of 5	1
MIR4500HG	ENST00000441617.7	n.489+25990A>G		intron_variant	Intron 1 of 3	3
MIR4500HG	ENST00000453832.2	n.272-23688A>G		intron_variant	Intron 1 of 3	3

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

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.484

Alfa AF: 0.394 Hom.: 6708

Bravo AF: 0.500

Asia WGS AF: 0.779 AC: 2697 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs979969; hg19: chr13-88297101;