Variant rs17625497 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001281746.2(MLIP):c.17G>A(p.Arg6His) variant causes a missense change. The variant allele was found at a frequency of 0.258 in 1,606,772 control chromosomes in the GnomAD database, including 56,579 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5203 hom., cov: 32)

Exomes 𝑓: 0.26 ( 51376 hom. )

Consequence

MLIP
NM_001281746.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.76

Variant links:

Genes affected

MLIP (HGNC:21355): (muscular LMNA interacting protein) Predicted to enable lamin binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of cardiac muscle hypertrophy in response to stress; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nuclear lumen. Predicted to be active in PML body; nuclear envelope; and sarcolemma. [provided by Alliance of Genome Resources, Apr 2022]

MLIP links:

MLIP-AS1 (HGNC:):

MLIP-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018709004).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
MLIP	NM_001281746.2 linkuse as main transcript	c.17G>A	p.Arg6His	missense_variant	1/12	NP_001268675.1	Q5VWP3-4
MLIP	NM_138569.3 linkuse as main transcript	c.17G>A	p.Arg6His	missense_variant	1/13	NP_612636.2	Q5VWP3-1
MLIP	XM_005249476.6 linkuse as main transcript	c.17G>A	p.Arg6His	missense_variant	1/14	XP_005249533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
MLIP	ENST00000514921.5 linkuse as main transcript	c.17G>A	p.Arg6His	missense_variant	1/12	1	ENSP00000425142.1	Q5VWP3-4
MLIP	ENST00000274897.9 linkuse as main transcript	c.17G>A	p.Arg6His	missense_variant	1/13	2	ENSP00000274897.5	Q5VWP3-1
MLIP	ENST00000370877.6 linkuse as main transcript	c.17G>A	p.Arg6His	missense_variant	1/8	5	ENSP00000359914.2	E2QRH6

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38183

AN:

151756

Hom.:

5203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.384

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.0625

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.278

GnomAD3 exomes

AF:

0.260

AC:

64894

AN:

249472

Hom.:

9383

AF XY:

0.254

AC XY:

34268

AN XY:

134824

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.408

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.0574

Gnomad SAS exome

AF:

0.178

Gnomad FIN exome

AF:

0.284

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.284

GnomAD4 exome

AF:

0.259

AC:

376968

AN:

1454900

Hom.:

51376

Cov.:

AF XY:

0.257

AC XY:

185866

AN XY:

724046

show subpopulations

Gnomad4 AFR exome

AF:

0.185

Gnomad4 AMR exome

AF:

0.406

Gnomad4 ASJ exome

AF:

0.263

Gnomad4 EAS exome

AF:

0.0796

Gnomad4 SAS exome

AF:

0.182

Gnomad4 FIN exome

AF:

0.283

Gnomad4 NFE exome

AF:

0.267

Gnomad4 OTH exome

AF:

0.252

GnomAD4 genome

AF:

0.252

AC:

38200

AN:

151872

Hom.:

5203

Cov.:

AF XY:

0.252

AC XY:

18740

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.190

Gnomad4 AMR

AF:

0.385

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.0626

Gnomad4 SAS

AF:

0.165

Gnomad4 FIN

AF:

0.287

Gnomad4 NFE

AF:

0.271

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.271

Hom.:

11934

Bravo

AF:

0.260

TwinsUK

AF:

0.261

AC:

966

ALSPAC

AF:

0.262

AC:

1008

ESP6500AA

AF:

0.182

AC:

804

ESP6500EA

AF:

0.281

AC:

2418

ExAC

AF:

0.252

AC:

30648

Asia WGS

AF:

0.152

AC:

529

AN:

3478

EpiCase

AF:

0.278

EpiControl

AF:

0.279

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.81

DEOGEN2

Benign

0.0029

.;T;T;.

Eigen

Benign

-0.85

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.045

LIST_S2

Benign

0.59

T;T;T;T

MetaRNN

Benign

0.0019

T;T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-0.90

N;N;.;.

PROVEAN

Benign

1.8

N;N;N;N

REVEL

Benign

0.092

Sift

Benign

0.35

T;T;T;T

Sift4G

Benign

0.45

T;T;T;T

Polyphen

0.0

.;B;.;.

Vest4

0.097

MPC

0.011

ClinPred

0.021

GERP RS

3.5

Varity_R

0.031

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over