Genetic Variant YY1:c.*4907A>C (chr14-100282507-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003403.5(YY1):c.*4907A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,156 control chromosomes in the GnomAD database, including 61,813 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 0.89 ( 61809 hom., cov: 31)

Exomes 𝑓: 1.0 ( 4 hom. )

Consequence

YY1
NM_003403.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.766

Publications

3 publications found

Variant links:

Genes affected

YY1 (HGNC:12856): (YY1 transcription factor) YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1. [provided by RefSeq, Jul 2008]

YY1 links:

ENSG00000259052 (HGNC:):

ENSG00000259052 links:

SLC25A29 (HGNC:20116): (solute carrier family 25 member 29) This gene encodes a nuclear-encoded mitochondrial protein that is a member of the large family of solute carrier family 25 (SLC25) mitochondrial transporters. The members of this superfamily are involved in numerous metabolic pathways and cell functions. This gene product was previously reported to be a mitochondrial carnitine-acylcarnitine-like (CACL) translocase (PMID:128829710) or an ornithine transporter (designated ORNT3, PMID:19287344), however, a recent study characterized the main role of this protein as a mitochondrial transporter of basic amino acids, with a preference for arginine and lysine (PMID:24652292). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]

SLC25A29 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YY1	NM_003403.5 link	c.*4907A>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000262238.10	NP_003394.1	P25490

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YY1	ENST00000262238.10 link	c.*4907A>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_003403.5	ENSP00000262238.4		P25490
ENSG00000259052	ENST00000553954.1 link	n.100-2442T>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.894

AC:

135912

AN:

152030

Hom.:

61765

Cov.:

show subpopulations

Gnomad AFR

AF:

0.709

Gnomad AMI

AF:

0.980

Gnomad AMR

AF:

0.943

Gnomad ASJ

AF:

0.964

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.971

Gnomad FIN

AF:

0.968

Gnomad MID

AF:

0.955

Gnomad NFE

AF:

0.964

Gnomad OTH

AF:

0.927

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.894

AC:

136012

AN:

152148

Hom.:

61809

Cov.:

AF XY:

0.898

AC XY:

66845

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.710

AC:

29418

AN:

41454

American (AMR)

AF:

0.943

AC:

14418

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.964

AC:

3346

AN:

3472

East Asian (EAS)

AF:

0.999

AC:

5162

AN:

5166

South Asian (SAS)

AF:

0.972

AC:

4676

AN:

4812

European-Finnish (FIN)

AF:

0.968

AC:

10280

AN:

10616

Middle Eastern (MID)

AF:

0.952

AC:

278

AN:

292

European-Non Finnish (NFE)

AF:

0.964

AC:

65583

AN:

68018

Other (OTH)

AF:

0.927

AC:

1957

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

637

1274

1911

2548

3185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.938

Hom.:

98270

Bravo

AF:

0.885

Asia WGS

AF:

0.972

AC:

3382

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.6

(source)

DANN

Benign

0.68

PhyloP100

-0.77

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over