rs9323592

Variant names:

• chr14-73755751-A-C
• rs9323592
• NM_001367710.1:c.-248+4012T>G

Variant summary

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

The NM_001367710.1(MIDEAS):​c.-248+4012T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,120 control chromosomes in the GnomAD database, including 1,667 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 0.10 (1667 hom., cov: 32)
• Consequence: MIDEAS NM_001367710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 1 publications found

Genes affected

MIDEAS (HGNC:19853): (mitotic deacetylase associated SANT domain protein) Predicted to enable transcription corepressor activity. Predicted to be involved in histone deacetylation; negative regulation of transcription, DNA-templated; and regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIDEAS	NM_001367710.1	MANE Select	c.-248+4012T>G		intron	N/A	NP_001354639.1	A0A1C7CYX1
	MIDEAS	NM_001394972.1		c.-247-15496T>G		intron	N/A	NP_001381901.1	A0A1C7CYX1
	MIDEAS	NM_001043318.3		c.-247-15496T>G		intron	N/A	NP_001036783.1	Q6PJG2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIDEAS	ENST00000423556.7	TSL:2 MANE Select	c.-248+4012T>G		intron	N/A	ENSP00000407767.2	A0A1C7CYX1
	MIDEAS	ENST00000286523.9	TSL:1	c.-248+4012T>G		intron	N/A	ENSP00000286523.5	Q6PJG2
	MIDEAS	ENST00000394071.6	TSL:1	c.-247-15496T>G		intron	N/A	ENSP00000377634.2	Q6PJG2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15863 AN: 152000 Hom.: 1662 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0374

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.105 AC: 15905 AN: 152120 Hom.: 1667 Cov.: 32 AF XY: 0.102 AC XY: 7584 AN XY: 74374

African (AFR) AF: 0.272 AC: 11257 AN: 41430

American (AMR) AF: 0.0796 AC: 1217 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0361 AC: 174 AN: 4824

European-Finnish (FIN) AF: 0.0205 AC: 218 AN: 10614

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0374 AC: 2542 AN: 67996

Other (OTH) AF: 0.102 AC: 215 AN: 2106

Alfa AF: 0.133 Hom.: 892

Bravo AF: 0.116

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9323592; hg19: chr14-74222454;