rs10486183

chr7-7564968-C-T

Variant summary

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

The NR_110084.1(MIOS-DT):n.153-644G>A variant causes a intron, non coding transcript 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 NR_110084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MIOS-DT	NR_110084.1	n.153-644G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIOS-DT	ENST00000609497.5	n.1083+946G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.00895

Gnomad4 FIN AF: 0.00284

Gnomad4 NFE AF: 0.00925

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0193 Hom.: 16

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

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;