GeneBe

NM_001410712.1:c.-29+6282T>G

Variant names:

Variant summary

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

The NM_001410712.1(SH3TC1):​c.-29+6282T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 152,322 control chromosomes in the GnomAD database, including 71,180 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 0.97 ( 71180 hom., cov: 35)

Consequence

SH3TC1
NM_001410712.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.306

Publications

1 publications found
Variant links:
Genes affected
SH3TC1 (HGNC:26009): (SH3 domain and tetratricopeptide repeats 1)

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=-0.99).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SH3TC1NM_001410712.1 linkc.-29+6282T>G intron_variant Intron 1 of 17 NP_001397641.1
SH3TC1XM_011513488.1 linkc.-29+6282T>G intron_variant Intron 1 of 17 XP_011511790.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SH3TC1ENST00000508641.2 linkc.-57+6282T>G intron_variant Intron 1 of 16 4 ENSP00000426035.2
SH3TC1ENST00000510763.5 linkn.139+6282T>G intron_variant Intron 1 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.966
AC:
147020
AN:
152204
Hom.:
71134
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.909
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.979
Gnomad ASJ
AF:
0.939
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.995
Gnomad FIN
AF:
0.999
Gnomad MID
AF:
0.949
Gnomad NFE
AF:
0.990
Gnomad OTH
AF:
0.951
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.966
AC:
147126
AN:
152322
Hom.:
71180
Cov.:
35
AF XY:
0.967
AC XY:
72005
AN XY:
74482
show subpopulations
African (AFR)
AF:
0.909
AC:
37760
AN:
41558
American (AMR)
AF:
0.979
AC:
14981
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
0.939
AC:
3261
AN:
3472
East Asian (EAS)
AF:
1.00
AC:
5167
AN:
5168
South Asian (SAS)
AF:
0.995
AC:
4804
AN:
4830
European-Finnish (FIN)
AF:
0.999
AC:
10620
AN:
10630
Middle Eastern (MID)
AF:
0.949
AC:
279
AN:
294
European-Non Finnish (NFE)
AF:
0.990
AC:
67333
AN:
68040
Other (OTH)
AF:
0.951
AC:
2009
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
246
492
738
984
1230
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
912
1824
2736
3648
4560
<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:
0.979
Hom.:
87111
Bravo
AF:
0.962
Asia WGS
AF:
0.991
AC:
3446
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.7
DANN
Benign
0.43
PhyloP100
-0.31

Splicing

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

Publications

Other links and lift over

dbSNP: rs1078701; hg19: chr4-8190219; API