Genetic Variant MKS1:c.*351delG (chr17-58205727-AC-A) – ACMG Classification: Benign (-10 pts)

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]

MKS1 links:

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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
MKS1	NM_017777.4 link	c.*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
MKS1	ENST00000393119 link	c.*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.:

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.:

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.:

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.:

Bravo

AF:

0.0347

Asia WGS

AF:

0.00549

AC:

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

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over