rs10236767

chr7-7572218-G-C

Variant summary

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

The NM_019005.4(MIOS):c.-40-218G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,022 control chromosomes in the GnomAD database, including 37,409 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 0.70 (37409 hom., cov: 32)
• Consequence: MIOS NM_019005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750

Genes affected

MIOS (HGNC:21905): (meiosis regulator for oocyte development) Involved in cellular response to amino acid starvation; positive regulation of TOR signaling; and protein-containing complex localization. Located in several cellular components, including cytosol; lysosomal membrane; and nucleoplasm. Part of GATOR2 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIOS	NM_019005.4	c.-40-218G>C		intron_variant		ENST00000340080.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIOS	ENST00000340080.9	c.-40-218G>C		intron_variant		1	NM_019005.4	P1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106497 AN: 151904 Hom.: 37372 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.701 AC: 106577 AN: 152022 Hom.: 37409 Cov.: 32 AF XY: 0.699 AC XY: 51907 AN XY: 74286

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.682

Alfa AF: 0.693 Hom.: 4514

Bravo AF: 0.712

Asia WGS AF: 0.609 AC: 2120 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	15
Dann	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10236767; hg19: chr7-7611849;