rs977357

Variant names:

• chr14-73744610-C-T
• rs977357
• NM_001367710.1:c.-247-4355G>A

Variant summary

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

The NM_001367710.1(MIDEAS):​c.-247-4355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,946 control chromosomes in the GnomAD database, including 13,468 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 0.40 (13468 hom., cov: 32)
• Consequence: MIDEAS NM_001367710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 3 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]

ENSG00000297421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIDEAS	NM_001367710.1	c.-247-4355G>A		intron_variant	Intron 1 of 12	ENST00000423556.7	NP_001354639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIDEAS	ENST00000423556.7	c.-247-4355G>A		intron_variant	Intron 1 of 12	2	NM_001367710.1	ENSP00000407767.2

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60738 AN: 151828 Hom.: 13441 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.400 AC: 60817 AN: 151946 Hom.: 13468 Cov.: 32 AF XY: 0.409 AC XY: 30364 AN XY: 74260

African (AFR) AF: 0.522 AC: 21608 AN: 41410

American (AMR) AF: 0.395 AC: 6038 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1334 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4100 AN: 5134

South Asian (SAS) AF: 0.595 AC: 2866 AN: 4818

European-Finnish (FIN) AF: 0.299 AC: 3159 AN: 10570

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20410 AN: 67948

Other (OTH) AF: 0.415 AC: 877 AN: 2112

Alfa AF: 0.370 Hom.: 1701

Bravo AF: 0.409

Asia WGS AF: 0.625 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.80
PhyloP100		0.029
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: rs977357; hg19: chr14-74211313;