rs10486183

Variant names:

• chr7-7564968-C-T
• rs10486183
• ENST00000609497.5:n.1083+946G>A

Variant summary

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

The ENST00000609497.5(MIOS-DT):​n.1083+946G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 151,942 control chromosomes in the GnomAD database, including 171 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 0.031 (171 hom., cov: 32)
• Consequence: MIOS-DT ENST00000609497.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

MIOS-DT (HGNC:55187): (MIOS divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIOS-DT	NR_110084.1	n.153-644G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIOS-DT	ENST00000609497.5	n.1083+946G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4652 AN: 151824 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.00936

Gnomad FIN AF: 0.00284

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00925

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0306 AC: 4655 AN: 151942 Hom.: 171 Cov.: 32 AF XY: 0.0300 AC XY: 2227 AN XY: 74254

Gnomad4 AFR AF: 0.0845 AC: 0.0844529 AN: 0.0844529

Gnomad4 AMR AF: 0.0212 AC: 0.021207 AN: 0.021207

Gnomad4 ASJ AF: 0.00115 AC: 0.0011534 AN: 0.0011534

Gnomad4 EAS AF: 0.0139 AC: 0.0139373 AN: 0.0139373

Gnomad4 SAS AF: 0.00895 AC: 0.00894715 AN: 0.00894715

Gnomad4 FIN AF: 0.00284 AC: 0.00284414 AN: 0.00284414

Gnomad4 NFE AF: 0.00925 AC: 0.00925272 AN: 0.00925272

Gnomad4 OTH AF: 0.0270 AC: 0.0270398 AN: 0.0270398

Alfa AF: 0.0209 Hom.: 23

Bravo AF: 0.0341

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.45
Mutation Taster		=100/0	polymorphism

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486183; hg19: chr7-7604599;