Variant chr6-16143159-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_013262.4(MYLIP):c.604A>C(p.Ile202Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0177 in 1,614,190 control chromosomes in the GnomAD database, including 304 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.014 ( 22 hom., cov: 32)

Exomes 𝑓: 0.018 ( 282 hom. )

Consequence

MYLIP
NM_013262.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.97

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]

MYLIP links:

MYLIP (HGNC:):

MYLIP links:

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=0.010784149).

BP6

Variant 6-16143159-A-C is Benign according to our data. Variant chr6-16143159-A-C is described in ClinVar as [Benign]. Clinvar id is 1599503.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-16143159-A-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0138 (2100/152308) while in subpopulation NFE AF= 0.0186 (1267/68026). AF 95% confidence interval is 0.0178. There are 22 homozygotes in gnomad4. There are 966 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 22 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYLIP	NM_013262.4 linkuse as main transcript	c.604A>C	p.Ile202Leu	missense_variant	4/7	ENST00000356840.8	NP_037394.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYLIP	ENST00000356840.8 linkuse as main transcript	c.604A>C	p.Ile202Leu	missense_variant	4/7	1	NM_013262.4	ENSP00000349298.3		Q8WY64-1
MYLIP	ENST00000349606.4 linkuse as main transcript	c.61A>C	p.Ile21Leu	missense_variant	3/6	1		ENSP00000008686.6		Q5TIA5

Frequencies

GnomAD3 genomes

AF:

0.0138

AC:

2102

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00307

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0171

Gnomad ASJ

AF:

0.0703

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0103

Gnomad FIN

AF:

0.00847

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0186

Gnomad OTH

AF:

0.0167

GnomAD3 exomes

AF:

0.0154

AC:

3876

AN:

251484

Hom.:

AF XY:

0.0157

AC XY:

2130

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00856

Gnomad ASJ exome

AF:

0.0680

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0120

Gnomad FIN exome

AF:

0.00975

Gnomad NFE exome

AF:

0.0192

Gnomad OTH exome

AF:

0.0145

GnomAD4 exome

AF:

0.0181

AC:

26493

AN:

1461882

Hom.:

282

Cov.:

AF XY:

0.0181

AC XY:

13151

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00227

Gnomad4 AMR exome

AF:

0.00923

Gnomad4 ASJ exome

AF:

0.0688

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0115

Gnomad4 FIN exome

AF:

0.0103

Gnomad4 NFE exome

AF:

0.0193

Gnomad4 OTH exome

AF:

0.0190

GnomAD4 genome

AF:

0.0138

AC:

2100

AN:

152308

Hom.:

Cov.:

AF XY:

0.0130

AC XY:

966

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00306

Gnomad4 AMR

AF:

0.0171

Gnomad4 ASJ

AF:

0.0703

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0101

Gnomad4 FIN

AF:

0.00847

Gnomad4 NFE

AF:

0.0186

Gnomad4 OTH

AF:

0.0166

Alfa

AF:

0.0197

Hom.:

Bravo

AF:

0.0141

TwinsUK

AF:

0.0181

AC:

ALSPAC

AF:

0.0189

AC:

ESP6500AA

AF:

0.00431

AC:

ESP6500EA

AF:

0.0199

AC:

171

ExAC

AF:

0.0149

AC:

1807

Asia WGS

AF:

0.00722

AC:

AN:

3478

EpiCase

AF:

0.0205

EpiControl

AF:

0.0219

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 25, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.34

T;.

Eigen

Benign

-0.34

Eigen_PC

Benign

-0.11

FATHMM_MKL

Uncertain

0.95

LIST_S2

Uncertain

0.92

D;D

MetaRNN

Benign

0.011

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.26

N;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-1.0

N;N

REVEL

Benign

0.056

Sift

Benign

0.080

T;T

Sift4G

Benign

0.39

T;T

Polyphen

0.0010

B;.

Vest4

0.59

MPC

0.17

ClinPred

0.026

GERP RS

4.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.39

gMVP

0.63

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