6-16145094-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_013262.4(MYLIP):ā€‹c.1025A>Gā€‹(p.Asn342Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 1,613,978 control chromosomes in the GnomAD database, including 237,883 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: š‘“ 0.63 ( 33294 hom., cov: 33)
Exomes š‘“: 0.51 ( 204589 hom. )

Consequence

MYLIP
NM_013262.4 missense

Scores

18

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.97
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=6.170516E-7).
BP6
Variant 6-16145094-A-G is Benign according to our data. Variant chr6-16145094-A-G is described in ClinVar as [Benign]. Clinvar id is 1598643.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-16145094-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYLIPNM_013262.4 linkuse as main transcriptc.1025A>G p.Asn342Ser missense_variant 6/7 ENST00000356840.8 NP_037394.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYLIPENST00000356840.8 linkuse as main transcriptc.1025A>G p.Asn342Ser missense_variant 6/71 NM_013262.4 ENSP00000349298.3 Q8WY64-1
MYLIPENST00000349606.4 linkuse as main transcriptc.482A>G p.Asn161Ser missense_variant 5/61 ENSP00000008686.6 Q5TIA5

Frequencies

GnomAD3 genomes
AF:
0.633
AC:
96171
AN:
152006
Hom.:
33227
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.897
Gnomad AMI
AF:
0.458
Gnomad AMR
AF:
0.644
Gnomad ASJ
AF:
0.517
Gnomad EAS
AF:
0.948
Gnomad SAS
AF:
0.653
Gnomad FIN
AF:
0.458
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.481
Gnomad OTH
AF:
0.589
GnomAD3 exomes
AF:
0.600
AC:
150922
AN:
251402
Hom.:
48765
AF XY:
0.587
AC XY:
79722
AN XY:
135872
show subpopulations
Gnomad AFR exome
AF:
0.905
Gnomad AMR exome
AF:
0.740
Gnomad ASJ exome
AF:
0.515
Gnomad EAS exome
AF:
0.949
Gnomad SAS exome
AF:
0.638
Gnomad FIN exome
AF:
0.469
Gnomad NFE exome
AF:
0.483
Gnomad OTH exome
AF:
0.560
GnomAD4 exome
AF:
0.515
AC:
752166
AN:
1461854
Hom.:
204589
Cov.:
72
AF XY:
0.516
AC XY:
375521
AN XY:
727224
show subpopulations
Gnomad4 AFR exome
AF:
0.912
Gnomad4 AMR exome
AF:
0.732
Gnomad4 ASJ exome
AF:
0.508
Gnomad4 EAS exome
AF:
0.966
Gnomad4 SAS exome
AF:
0.636
Gnomad4 FIN exome
AF:
0.482
Gnomad4 NFE exome
AF:
0.468
Gnomad4 OTH exome
AF:
0.545
GnomAD4 genome
AF:
0.633
AC:
96301
AN:
152124
Hom.:
33294
Cov.:
33
AF XY:
0.633
AC XY:
47055
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.897
Gnomad4 AMR
AF:
0.645
Gnomad4 ASJ
AF:
0.517
Gnomad4 EAS
AF:
0.948
Gnomad4 SAS
AF:
0.652
Gnomad4 FIN
AF:
0.458
Gnomad4 NFE
AF:
0.481
Gnomad4 OTH
AF:
0.593
Alfa
AF:
0.515
Hom.:
51541
Bravo
AF:
0.660
TwinsUK
AF:
0.462
AC:
1713
ALSPAC
AF:
0.466
AC:
1797
ESP6500AA
AF:
0.887
AC:
3906
ESP6500EA
AF:
0.476
AC:
4094
ExAC
AF:
0.606
AC:
73628
Asia WGS
AF:
0.835
AC:
2904
AN:
3478
EpiCase
AF:
0.468
EpiControl
AF:
0.468

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 testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.066
BayesDel_addAF
Benign
-0.63
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
5.9
DANN
Benign
0.64
DEOGEN2
Benign
0.029
T;.
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.015
N
LIST_S2
Benign
0.12
T;T
MetaRNN
Benign
6.2e-7
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-0.035
N;.
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-0.070
N;N
REVEL
Benign
0.14
Sift
Benign
1.0
T;T
Sift4G
Benign
0.66
T;T
Polyphen
0.0
B;.
Vest4
0.016
MPC
0.14
ClinPred
0.0018
T
GERP RS
3.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.034
gMVP
0.13

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: rs9370867; hg19: chr6-16145325; COSMIC: COSV62766341; COSMIC: COSV62766341; API