Variant rs2205794 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_013262.4(MYLIP):c.*1194G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 152,608 control chromosomes in the GnomAD database, including 162 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.034 ( 162 hom., cov: 32)

Exomes 𝑓: 0.021 ( 0 hom. )

Consequence

MYLIP
NM_013262.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.81

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYLIP	NM_013262.4 linkuse as main transcript	c.*1194G>A		3_prime_UTR_variant	7/7	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.*1194G>A		3_prime_UTR_variant	7/7	1	NM_013262.4	ENSP00000349298.3		Q8WY64-1
MYLIP	ENST00000349606.4 linkuse as main transcript	c.*1194G>A		3_prime_UTR_variant	6/6	1		ENSP00000008686.6		Q5TIA5

Frequencies

GnomAD3 genomes

AF:

0.0337

AC:

5124

AN:

152056

Hom.:

163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0164

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0247

Gnomad ASJ

AF:

0.0450

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.0560

Gnomad FIN

AF:

0.0168

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0354

Gnomad OTH

AF:

0.0364

GnomAD4 exome

AF:

0.0208

AC:

AN:

432

Hom.:

Cov.:

AF XY:

0.0231

AC XY:

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.0211

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0336

AC:

5118

AN:

152176

Hom.:

162

Cov.:

AF XY:

0.0335

AC XY:

2495

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0164

Gnomad4 AMR

AF:

0.0246

Gnomad4 ASJ

AF:

0.0450

Gnomad4 EAS

AF:

0.186

Gnomad4 SAS

AF:

0.0554

Gnomad4 FIN

AF:

0.0168

Gnomad4 NFE

AF:

0.0354

Gnomad4 OTH

AF:

0.0360

Alfa

AF:

0.0338

Hom.:

Bravo

AF:

0.0354

Asia WGS

AF:

0.103

AC:

359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.97

Splicing

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