ENST00000394071.6:c.-248+3090G>A

Variant names:

• chr14-73784012-C-T
• rs12878166
• ENST00000394071.6:c.-248+3090G>A

Variant summary

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

The ENST00000394071.6(MIDEAS):​c.-248+3090G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,056 control chromosomes in the GnomAD database, including 19,190 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 0.49 (19190 hom., cov: 32)
• Consequence: MIDEAS ENST00000394071.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIDEAS	NM_001394972.1	c.-248+3090G>A		intron_variant	Intron 1 of 12		NP_001381901.1
MIDEAS	NM_001043318.3	c.-248+3090G>A		intron_variant	Intron 1 of 11		NP_001036783.1
MIDEAS	XM_005268206.1	c.-248+5813G>A		intron_variant	Intron 2 of 13		XP_005268263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIDEAS	ENST00000394071.6	c.-248+3090G>A		intron_variant	Intron 1 of 11	1		ENSP00000377634.2
MIDEAS	ENST00000486739.1	n.309+5813G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73936 AN: 151938 Hom.: 19170 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.487 AC: 73990 AN: 152056 Hom.: 19190 Cov.: 32 AF XY: 0.496 AC XY: 36844 AN XY: 74332

African (AFR) AF: 0.568 AC: 23555 AN: 41464

American (AMR) AF: 0.507 AC: 7758 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1927 AN: 3466

East Asian (EAS) AF: 0.877 AC: 4537 AN: 5174

South Asian (SAS) AF: 0.728 AC: 3508 AN: 4818

European-Finnish (FIN) AF: 0.375 AC: 3960 AN: 10564

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26933 AN: 67958

Other (OTH) AF: 0.515 AC: 1087 AN: 2112

Alfa AF: 0.441 Hom.: 38938

Bravo AF: 0.497

Asia WGS AF: 0.761 AC: 2644 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	3.9
DANN	Benign	0.46
PhyloP100		-0.11
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: rs12878166; hg19: chr14-74250715;