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GeneBe

rs1060901

chr6-16145242-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_013262.4(MYLIP):c.1173C>T(p.Cys391=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 1,613,460 control chromosomes in the GnomAD database, including 6,079 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.062 ( 374 hom., cov: 32)
Exomes 𝑓: 0.084 ( 5705 hom. )

Consequence

MYLIP
NM_013262.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.201
Variant links:
Genes affected
MYLIP (HGNC:21155): (myosin regulatory light chain interacting protein) The ERM protein family members ezrin, radixin, and moesin are cytoskeletal effector proteins linking actin to membrane-bound proteins at the cell surface. Myosin regulatory light chain interacting protein (MYLIP) is a novel ERM-like protein that interacts with myosin regulatory light chain and inhibits neurite outgrowth. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-16145242-C-T is Benign according to our data. Variant chr6-16145242-C-T is described in ClinVar as [Benign]. Clinvar id is 1601611.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-16145242-C-T is described in Lovd as [Benign].
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.201 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0931 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYLIPNM_013262.4 linkuse as main transcriptc.1173C>T p.Cys391= synonymous_variant 6/7 ENST00000356840.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYLIPENST00000356840.8 linkuse as main transcriptc.1173C>T p.Cys391= synonymous_variant 6/71 NM_013262.4 P1Q8WY64-1
MYLIPENST00000349606.4 linkuse as main transcriptc.630C>T p.Cys210= synonymous_variant 5/61

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0622
AC:
9459
AN:
152120
Hom.:
374
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0157
Gnomad AMI
AF:
0.0713
Gnomad AMR
AF:
0.0420
Gnomad ASJ
AF:
0.0545
Gnomad EAS
AF:
0.00116
Gnomad SAS
AF:
0.0238
Gnomad FIN
AF:
0.112
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0950
Gnomad OTH
AF:
0.0564
GnomAD3 exomes
AF:
0.0658
AC:
16497
AN:
250772
Hom.:
732
AF XY:
0.0660
AC XY:
8955
AN XY:
135584
show subpopulations
Gnomad AFR exome
AF:
0.0131
Gnomad AMR exome
AF:
0.0332
Gnomad ASJ exome
AF:
0.0572
Gnomad EAS exome
AF:
0.000218
Gnomad SAS exome
AF:
0.0255
Gnomad FIN exome
AF:
0.120
Gnomad NFE exome
AF:
0.0950
Gnomad OTH exome
AF:
0.0712
GnomAD4 exome
AF:
0.0841
AC:
122866
AN:
1461222
Hom.:
5705
Cov.:
34
AF XY:
0.0826
AC XY:
60005
AN XY:
726798
show subpopulations
Gnomad4 AFR exome
AF:
0.0132
Gnomad4 AMR exome
AF:
0.0345
Gnomad4 ASJ exome
AF:
0.0563
Gnomad4 EAS exome
AF:
0.000378
Gnomad4 SAS exome
AF:
0.0255
Gnomad4 FIN exome
AF:
0.121
Gnomad4 NFE exome
AF:
0.0955
Gnomad4 OTH exome
AF:
0.0732
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0621
AC:
9454
AN:
152238
Hom.:
374
Cov.:
32
AF XY:
0.0610
AC XY:
4539
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0156
Gnomad4 AMR
AF:
0.0420
Gnomad4 ASJ
AF:
0.0545
Gnomad4 EAS
AF:
0.00116
Gnomad4 SAS
AF:
0.0234
Gnomad4 FIN
AF:
0.112
Gnomad4 NFE
AF:
0.0950
Gnomad4 OTH
AF:
0.0549
Alfa
AF:
0.0817
Hom.:
291
Bravo
AF:
0.0553
Asia WGS
AF:
0.0140
AC:
48
AN:
3478
EpiCase
AF:
0.0884
EpiControl
AF:
0.0849

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
3.8
Dann
Benign
0.82
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs1060901; hg19: chr6-16145473; COSMIC: COSV62766793; COSMIC: COSV62766793; API