Genetic Variant NM_003173.4:c.*1334G>A (chrX-48708904-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003173.4(SUV39H1):c.*1334G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.62 ( 16478 hom., 18800 hem., cov: 21)

Exomes 𝑓: 0.67 ( 5 hom. 15 hem. )

Failed GnomAD Quality Control

Consequence

SUV39H1
NM_003173.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.312

Publications

11 publications found

Variant links:

Genes affected

SUV39H1 (HGNC:11479): (SUV39H1 histone lysine methyltransferase) This gene encodes an evolutionarily-conserved protein containing an N-terminal chromodomain and a C-terminal SET domain. The encoded protein is a histone methyltransferase that trimethylates lysine 9 of histone H3, which results in transcriptional gene silencing. Loss of function of this gene disrupts heterochromatin formation and may cause chromosome instability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

SUV39H1 links:

ENSG00000232828 (HGNC:):

ENSG00000232828 links:

Genome browser will be placed here

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=-0.9).

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003173.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUV39H1	NM_003173.4	MANE Select	c.*1334G>A		3_prime_UTR	Exon 6 of 6	NP_003164.1	O43463-1
	SUV39H1	NM_001282166.2		c.*1334G>A		3_prime_UTR	Exon 6 of 6	NP_001269095.1	O43463-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SUV39H1	ENST00000376687.4	TSL:1 MANE Select	c.*1334G>A	3_prime_UTR	Exon 6 of 6	ENSP00000365877.4	O43463-1
SUV39H1	ENST00000337852.10	TSL:2	c.*1334G>A	3_prime_UTR	Exon 6 of 6	ENSP00000337976.6	O43463-2
SUV39H1	ENST00000936593.1		c.*1334G>A	3_prime_UTR	Exon 6 of 6	ENSP00000606652.1

Frequencies

GnomAD3 genomes

AF:

0.617

AC:

66877

AN:

108402

Hom.:

16486

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.857

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.778

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.848

Gnomad NFE

AF:

0.740

Gnomad OTH

AF:

0.671

GnomAD4 exome

AF:

0.674

AC:

AN:

Hom.:

Cov.:

AF XY:

0.652

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.700

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.720

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.617

AC:

66885

AN:

108453

Hom.:

16478

Cov.:

AF XY:

0.609

AC XY:

18800

AN XY:

30857

show subpopulations

African (AFR)

AF:

0.308

AC:

9217

AN:

29899

American (AMR)

AF:

0.713

AC:

7311

AN:

10261

Ashkenazi Jewish (ASJ)

AF:

0.778

AC:

2025

AN:

2603

East Asian (EAS)

AF:

0.834

AC:

2834

AN:

3397

South Asian (SAS)

AF:

0.648

AC:

1553

AN:

2395

European-Finnish (FIN)

AF:

0.673

AC:

3724

AN:

5531

Middle Eastern (MID)

AF:

0.843

AC:

182

AN:

216

European-Non Finnish (NFE)

AF:

0.740

AC:

38490

AN:

52020

Other (OTH)

AF:

0.669

AC:

986

AN:

1474

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

729

1458

2187

2916

3645

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

586

1172

1758

2344

2930

<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:

0.698

Hom.:

93345

Bravo

AF:

0.618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over