17-58205727-AC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_017777.4(MKS1):​c.*351delG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.051 in 1,352,134 control chromosomes in the GnomAD database, including 2,171 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.039 ( 190 hom., cov: 31)
Exomes 𝑓: 0.053 ( 1981 hom. )

Consequence

MKS1
NM_017777.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.160
Variant links:
Genes affected
MKS1 (HGNC:7121): (MKS transition zone complex subunit 1) The protein encoded by this gene localizes to the basal body and is required for formation of the primary cilium in ciliated epithelial cells. Mutations in this gene result in Meckel syndrome type 1 and in Bardet-Biedl syndrome type 13. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 17-58205727-AC-A is Benign according to our data. Variant chr17-58205727-AC-A is described in ClinVar as [Benign]. Clinvar id is 1277626.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-58205727-AC-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MKS1NM_017777.4 linkc.*351delG 3_prime_UTR_variant Exon 18 of 18 ENST00000393119.7 NP_060247.2 Q9NXB0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MKS1ENST00000393119 linkc.*351delG 3_prime_UTR_variant Exon 18 of 18 1 NM_017777.4 ENSP00000376827.2 Q9NXB0-1

Frequencies

GnomAD3 genomes
AF:
0.0389
AC:
5925
AN:
152148
Hom.:
190
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00929
Gnomad AMI
AF:
0.0912
Gnomad AMR
AF:
0.0264
Gnomad ASJ
AF:
0.0170
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00828
Gnomad FIN
AF:
0.0625
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0619
Gnomad OTH
AF:
0.0393
GnomAD3 exomes
AF:
0.0365
AC:
5531
AN:
151520
Hom.:
152
AF XY:
0.0349
AC XY:
2837
AN XY:
81366
show subpopulations
Gnomad AFR exome
AF:
0.00753
Gnomad AMR exome
AF:
0.0228
Gnomad ASJ exome
AF:
0.0141
Gnomad EAS exome
AF:
0.0000927
Gnomad SAS exome
AF:
0.00671
Gnomad FIN exome
AF:
0.0630
Gnomad NFE exome
AF:
0.0598
Gnomad OTH exome
AF:
0.0370
GnomAD4 exome
AF:
0.0525
AC:
63008
AN:
1199868
Hom.:
1981
Cov.:
30
AF XY:
0.0506
AC XY:
29805
AN XY:
588612
show subpopulations
Gnomad4 AFR exome
AF:
0.00686
Gnomad4 AMR exome
AF:
0.0223
Gnomad4 ASJ exome
AF:
0.0158
Gnomad4 EAS exome
AF:
0.000239
Gnomad4 SAS exome
AF:
0.00754
Gnomad4 FIN exome
AF:
0.0633
Gnomad4 NFE exome
AF:
0.0605
Gnomad4 OTH exome
AF:
0.0387
GnomAD4 genome
AF:
0.0389
AC:
5925
AN:
152266
Hom.:
190
Cov.:
31
AF XY:
0.0379
AC XY:
2820
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.00927
Gnomad4 AMR
AF:
0.0263
Gnomad4 ASJ
AF:
0.0170
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00829
Gnomad4 FIN
AF:
0.0625
Gnomad4 NFE
AF:
0.0619
Gnomad4 OTH
AF:
0.0389
Alfa
AF:
0.0323
Hom.:
28
Bravo
AF:
0.0347
Asia WGS
AF:
0.00549
AC:
19
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 14, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

LitVar

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

Other links and lift over

dbSNP: rs35298266; hg19: chr17-56283088; API