rs563630291

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The variant allele was found at a frequency of 0.0104 in 318,044 control chromosomes in the GnomAD database, including 28 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0097 ( 10 hom., cov: 33)
Exomes 𝑓: 0.011 ( 18 hom. )

Consequence

Unknown

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.66
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP6
Variant 11-2161296-TG-T is Benign according to our data. Variant chr11-2161296-TG-T is described in ClinVar as [Benign]. Clinvar id is 435506.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.00967
AC:
1470
AN:
152010
Hom.:
10
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00210
Gnomad AMI
AF:
0.0241
Gnomad AMR
AF:
0.00714
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00311
Gnomad FIN
AF:
0.0259
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0138
Gnomad OTH
AF:
0.00860
GnomAD4 exome
AF:
0.0110
AC:
1833
AN:
165916
Hom.:
18
Cov.:
0
AF XY:
0.0109
AC XY:
913
AN XY:
83750
show subpopulations
Gnomad4 AFR exome
AF:
0.00238
Gnomad4 AMR exome
AF:
0.00497
Gnomad4 ASJ exome
AF:
0.000333
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00535
Gnomad4 FIN exome
AF:
0.0260
Gnomad4 NFE exome
AF:
0.0134
Gnomad4 OTH exome
AF:
0.00988
GnomAD4 genome
AF:
0.00966
AC:
1469
AN:
152128
Hom.:
10
Cov.:
33
AF XY:
0.0103
AC XY:
764
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.00210
Gnomad4 AMR
AF:
0.00713
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00311
Gnomad4 FIN
AF:
0.0259
Gnomad4 NFE
AF:
0.0138
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.0110
Hom.:
3
Bravo
AF:
0.00762
Asia WGS
AF:
0.00202
AC:
7
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxMar 25, 2019- -
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenSep 01, 2024INS-IGF2: BS1, BS2 -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoOct 31, 2016- -
Neonatal insulin-dependent diabetes mellitus Benign:1
Benign, criteria provided, single submitterresearchClinical Genomics, Uppaluri K&H Personalized Medicine Clinic-Mutations in INS gene can cause early onset diabetes mellitus which is insulin dependent. May have poor response to sulfonylureas, as this mutation can cause beta cell destruction. However no sufficient evidence is found to ascertain the role of this particular variant rs563630291, yet. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs563630291; hg19: chr11-2182526; API