GeneBe

NM_018986.5:c.1244-328G>C

Variant names:

Variant summary

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

The NM_018986.5(SH3TC1):​c.1244-328G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,086 control chromosomes in the GnomAD database, including 11,727 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 0.39 ( 11727 hom., cov: 33)

Consequence

SH3TC1
NM_018986.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470

Publications

2 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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SH3TC1NM_018986.5 linkc.1244-328G>C intron_variant Intron 10 of 17 ENST00000245105.8 NP_061859.4 Q8TE82B3KWX8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SH3TC1ENST00000245105.8 linkc.1244-328G>C intron_variant Intron 10 of 17 2 NM_018986.5 ENSP00000245105.3 Q8TE82

Frequencies

GnomAD3 genomes
AF:
0.386
AC:
58652
AN:
151970
Hom.:
11719
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.436
Gnomad AMI
AF:
0.307
Gnomad AMR
AF:
0.480
Gnomad ASJ
AF:
0.346
Gnomad EAS
AF:
0.537
Gnomad SAS
AF:
0.301
Gnomad FIN
AF:
0.407
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.330
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.386
AC:
58693
AN:
152086
Hom.:
11727
Cov.:
33
AF XY:
0.391
AC XY:
29093
AN XY:
74360
show subpopulations
African (AFR)
AF:
0.435
AC:
18051
AN:
41468
American (AMR)
AF:
0.480
AC:
7341
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.346
AC:
1200
AN:
3472
East Asian (EAS)
AF:
0.537
AC:
2767
AN:
5156
South Asian (SAS)
AF:
0.302
AC:
1458
AN:
4828
European-Finnish (FIN)
AF:
0.407
AC:
4315
AN:
10596
Middle Eastern (MID)
AF:
0.276
AC:
81
AN:
294
European-Non Finnish (NFE)
AF:
0.330
AC:
22423
AN:
67974
Other (OTH)
AF:
0.370
AC:
779
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1878
3756
5634
7512
9390
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
544
1088
1632
2176
2720
<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:
0.215
Hom.:
458
Bravo
AF:
0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.9
DANN
Benign
0.58
PhyloP100
0.47
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: rs2279195; hg19: chr4-8226574; API