rs9323592

chr14-73755751-A-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIDEAS	NM_001367710.1	c.-248+4012T>G		intron_variant		ENST00000423556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIDEAS	ENST00000423556.7	c.-248+4012T>G		intron_variant		2	NM_001367710.1	P1
MIDEAS	ENST00000286523.9	c.-248+4012T>G		intron_variant		1
MIDEAS	ENST00000394071.6	c.-247-15496T>G		intron_variant		1
MIDEAS	ENST00000486739.1	n.310-15496T>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.0796

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.0374

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0784 Hom.: 142

Bravo AF: 0.116

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	11
Dann	Benign	0.71

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: rs9323592; hg19: chr14-74222454;