rs17168704

chr7-7564445-C-G

Variant summary

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

The NR_110084.1(MIOS-DT):n.153-121G>C 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 0.111 in 152,142 control chromosomes in the GnomAD database, including 2,827 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 0.11 (2826 hom., cov: 33)
  • Exomes 𝑓: 0.067 (1 hom.)
• Consequence: MIOS-DT NR_110084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIOS-DT	NR_110084.1	n.153-121G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIOS-DT	ENST00000609497.5	n.1083+1469G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16894 AN: 151994 Hom.: 2818 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00293

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0901

GnomAD4 exome AF: 0.0667 AC: 2 AN: 30 Hom.: 1 AF XY: 0.00 AC XY: 0 AN XY: 24

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.111 AC: 16943 AN: 152112 Hom.: 2826 Cov.: 33 AF XY: 0.109 AC XY: 8113 AN XY: 74382

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0102

Gnomad4 FIN AF: 0.00293

Gnomad4 NFE AF: 0.0105

Gnomad4 OTH AF: 0.0887

Alfa AF: 0.0703 Hom.: 187

Bravo AF: 0.125

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.24
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17168704; hg19: chr7-7604076;