14-73744610-C-T

Position:

• chr14-73744610-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC124903345 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MIDEAS	NM_001367710.1	c.-247-4355G>A		intron_variant		ENST00000423556.7
LOC124903345	XR_007064264.1	n.182+602C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIDEAS	ENST00000423556.7	c.-247-4355G>A		intron_variant		2	NM_001367710.1	P1

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

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.415

Alfa AF: 0.365 Hom.: 1593

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

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: rs977357; hg19: chr14-74211313;