Variant 6-152721788-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_025107.3(MYCT1):c.243A>T(p.Val81Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00747 in 1,614,050 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0058 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0076 ( 61 hom. )

Consequence

MYCT1
NM_025107.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.25

Variant links:

Genes affected

MYCT1 (HGNC:23172): (MYC target 1) Predicted to act upstream of or within hematopoietic stem cell homeostasis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MYCT1 links:

MYCT1 (HGNC:):

MYCT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 6-152721788-A-T is Benign according to our data. Variant chr6-152721788-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 3024889.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.25 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYCT1	NM_025107.3 linkuse as main transcript	c.243A>T	p.Val81Val	synonymous_variant	2/2	ENST00000367245.6	NP_079383.2	Q8N699

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MYCT1	ENST00000367245.6 linkuse as main transcript	c.243A>T	p.Val81Val	synonymous_variant	2/2	1	NM_025107.3	ENSP00000356214.5	Q8N699
MYCT1	ENST00000532295.1 linkuse as main transcript	c.183A>T	p.Val61Val	synonymous_variant	2/3	3		ENSP00000434396.1	H0YDV5
MYCT1	ENST00000529453.1 linkuse as main transcript	c.197-975A>T		intron_variant		3		ENSP00000432612.1	E9PQ55

Frequencies

GnomAD3 genomes

AF:

0.00579

AC:

880

AN:

152074

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00196

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00799

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00920

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00508

AC:

1277

AN:

251326

Hom.:

AF XY:

0.00530

AC XY:

720

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.00197

Gnomad AMR exome

AF:

0.00417

Gnomad ASJ exome

AF:

0.00576

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000882

Gnomad FIN exome

AF:

0.00194

Gnomad NFE exome

AF:

0.00820

Gnomad OTH exome

AF:

0.00686

GnomAD4 exome

AF:

0.00765

AC:

11176

AN:

1461858

Hom.:

Cov.:

AF XY:

0.00742

AC XY:

5395

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.00161

Gnomad4 AMR exome

AF:

0.00443

Gnomad4 ASJ exome

AF:

0.00685

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000765

Gnomad4 FIN exome

AF:

0.00180

Gnomad4 NFE exome

AF:

0.00909

Gnomad4 OTH exome

AF:

0.00748

GnomAD4 genome

AF:

0.00578

AC:

880

AN:

152192

Hom.:

Cov.:

AF XY:

0.00540

AC XY:

402

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.00195

Gnomad4 AMR

AF:

0.00798

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00189

Gnomad4 NFE

AF:

0.00920

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00691

Hom.:

Bravo

AF:

0.00591

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00921

EpiControl

AF:

0.00948

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2023

MYCT1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.27

DANN

Benign

0.63

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over