chr10-95510972-C-T

Variant summary

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

The NM_001034954.3(SORBS1):​c.-131-19852G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,192 control chromosomes in the GnomAD database, including 693 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 0.087 ( 693 hom., cov: 32)

Consequence

SORBS1
NM_001034954.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.187

Publications

6 publications found
Variant links:
Genes affected
SORBS1 (HGNC:14565): (sorbin and SH3 domain containing 1) This gene encodes a CBL-associated protein which functions in the signaling and stimulation of insulin. Mutations in this gene may be associated with human disorders of insulin resistance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SORBS1NM_001034954.3 linkc.-131-19852G>A intron_variant Intron 1 of 32 ENST00000371247.7 NP_001030126.2 Q9BX66-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SORBS1ENST00000371247.7 linkc.-131-19852G>A intron_variant Intron 1 of 32 5 NM_001034954.3 ENSP00000360293.2 Q9BX66-1

Frequencies

GnomAD3 genomes
AF:
0.0873
AC:
13279
AN:
152074
Hom.:
691
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0726
Gnomad AMI
AF:
0.0164
Gnomad AMR
AF:
0.0820
Gnomad ASJ
AF:
0.0597
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0141
Gnomad FIN
AF:
0.153
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.102
Gnomad OTH
AF:
0.0857
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0873
AC:
13290
AN:
152192
Hom.:
693
Cov.:
32
AF XY:
0.0869
AC XY:
6463
AN XY:
74396
show subpopulations
African (AFR)
AF:
0.0727
AC:
3020
AN:
41526
American (AMR)
AF:
0.0819
AC:
1252
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.0597
AC:
207
AN:
3470
East Asian (EAS)
AF:
0.000193
AC:
1
AN:
5180
South Asian (SAS)
AF:
0.0139
AC:
67
AN:
4826
European-Finnish (FIN)
AF:
0.153
AC:
1620
AN:
10588
Middle Eastern (MID)
AF:
0.0408
AC:
12
AN:
294
European-Non Finnish (NFE)
AF:
0.102
AC:
6917
AN:
68000
Other (OTH)
AF:
0.0848
AC:
179
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
589
1178
1767
2356
2945
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
142
284
426
568
710
<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:
0.0906
Hom.:
1306
Bravo
AF:
0.0820
Asia WGS
AF:
0.0130
AC:
46
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.3
DANN
Benign
0.68
PhyloP100
-0.19
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: rs12247017; hg19: chr10-97270729; API