rs17382306
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_203349.4(SHC4):c.1304-241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,972 control chromosomes in the GnomAD database, including 2,374 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 0.17 ( 2374 hom., cov: 32)
Consequence
SHC4
NM_203349.4 intron
NM_203349.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.144
Publications
0 publications found
Genes affected
SHC4 (HGNC:16743): (SHC adaptor protein 4) Predicted to enable receptor tyrosine kinase binding activity. Predicted to be involved in transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to act upstream of or within several processes, including apoptotic process; positive regulation of cell population proliferation; and stem cell differentiation. Predicted to be located in postsynaptic membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHC4 | NM_203349.4 | c.1304-241C>T | intron_variant | Intron 9 of 11 | ENST00000332408.9 | NP_976224.3 | ||
SHC4 | XM_005254375.4 | c.755-241C>T | intron_variant | Intron 9 of 11 | XP_005254432.1 | |||
SHC4 | XM_047432492.1 | c.446-241C>T | intron_variant | Intron 6 of 8 | XP_047288448.1 | |||
SHC4 | XM_047432493.1 | c.446-241C>T | intron_variant | Intron 7 of 9 | XP_047288449.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHC4 | ENST00000332408.9 | c.1304-241C>T | intron_variant | Intron 9 of 11 | 1 | NM_203349.4 | ENSP00000329668.4 | |||
SHC4 | ENST00000396535.7 | c.575-241C>T | intron_variant | Intron 6 of 8 | 1 | ENSP00000379786.3 | ||||
SHC4 | ENST00000537958.5 | c.446-241C>T | intron_variant | Intron 7 of 9 | 2 | ENSP00000443300.1 | ||||
SHC4 | ENST00000557797.5 | n.385-241C>T | intron_variant | Intron 5 of 6 | 3 | ENSP00000453344.1 |
Frequencies
GnomAD3 genomes AF: 0.168 AC: 25484AN: 151854Hom.: 2374 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
25484
AN:
151854
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.168 AC: 25506AN: 151972Hom.: 2374 Cov.: 32 AF XY: 0.166 AC XY: 12303AN XY: 74242 show subpopulations
GnomAD4 genome
AF:
AC:
25506
AN:
151972
Hom.:
Cov.:
32
AF XY:
AC XY:
12303
AN XY:
74242
show subpopulations
African (AFR)
AF:
AC:
4179
AN:
41460
American (AMR)
AF:
AC:
2288
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
690
AN:
3472
East Asian (EAS)
AF:
AC:
415
AN:
5170
South Asian (SAS)
AF:
AC:
805
AN:
4818
European-Finnish (FIN)
AF:
AC:
2061
AN:
10504
Middle Eastern (MID)
AF:
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14432
AN:
67964
Other (OTH)
AF:
AC:
334
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1041
2081
3122
4162
5203
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
288
576
864
1152
1440
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
534
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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