GeneBe

NM_052928.3:c.135-6904G>A

Variant names:

Variant summary

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

The NM_052928.3(SMYD4):​c.135-6904G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,694 control chromosomes in the GnomAD database, including 2,779 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 0.19 ( 2779 hom., cov: 30)

Consequence

SMYD4
NM_052928.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.970

Publications

2 publications found
Variant links:
Genes affected
SMYD4 (HGNC:21067): (SET and MYND domain containing 4) Predicted to enable metal ion binding activity and methyltransferase activity. Involved in heart development. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SMYD4NM_052928.3 linkc.135-6904G>A intron_variant Intron 2 of 10 ENST00000305513.12 NP_443160.2 Q8IYR2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SMYD4ENST00000305513.12 linkc.135-6904G>A intron_variant Intron 2 of 10 1 NM_052928.3 ENSP00000304360.7 Q8IYR2

Frequencies

GnomAD3 genomes
AF:
0.188
AC:
28570
AN:
151576
Hom.:
2783
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.202
Gnomad AMI
AF:
0.175
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.183
Gnomad EAS
AF:
0.130
Gnomad SAS
AF:
0.125
Gnomad FIN
AF:
0.161
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.199
Gnomad OTH
AF:
0.202
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.188
AC:
28576
AN:
151694
Hom.:
2779
Cov.:
30
AF XY:
0.184
AC XY:
13663
AN XY:
74110
show subpopulations
African (AFR)
AF:
0.202
AC:
8336
AN:
41316
American (AMR)
AF:
0.162
AC:
2463
AN:
15204
Ashkenazi Jewish (ASJ)
AF:
0.183
AC:
635
AN:
3472
East Asian (EAS)
AF:
0.130
AC:
674
AN:
5168
South Asian (SAS)
AF:
0.125
AC:
601
AN:
4802
European-Finnish (FIN)
AF:
0.161
AC:
1695
AN:
10496
Middle Eastern (MID)
AF:
0.204
AC:
60
AN:
294
European-Non Finnish (NFE)
AF:
0.199
AC:
13529
AN:
67922
Other (OTH)
AF:
0.201
AC:
424
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1159
2318
3477
4636
5795
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
306
612
918
1224
1530
<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:
0.194
Hom.:
1135
Bravo
AF:
0.191
Asia WGS
AF:
0.141
AC:
489
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
2.5
DANN
Benign
0.49
PhyloP100
-0.97
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

Publications

Other links and lift over

dbSNP: rs12601246; hg19: chr17-1722313; API