dbSNP rs2205794: MYLIP:c.*1194G>A (chr6-16147945-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

3 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013262.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYLIP	NM_013262.4	MANE Select	c.*1194G>A		3_prime_UTR	Exon 7 of 7	NP_037394.2
	MYLIP	NM_001436627.1		c.*1194G>A		3_prime_UTR	Exon 6 of 6	NP_001423556.1	A0ABB0MVD9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYLIP	ENST00000356840.8	TSL:1 MANE Select	c.*1194G>A	3_prime_UTR	Exon 7 of 7	ENSP00000349298.3	Q8WY64-1
MYLIP	ENST00000349606.5	TSL:1	n.*2116G>A	non_coding_transcript_exon	Exon 6 of 6	ENSP00000008686.6	Q5TIA5
MYLIP	ENST00000349606.5	TSL:1	n.*2116G>A	3_prime_UTR	Exon 6 of 6	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

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0211

AC:

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.414

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0336

AC:

5118

AN:

152176

Hom.:

162

Cov.:

AF XY:

0.0335

AC XY:

2495

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0164

AC:

679

AN:

41504

American (AMR)

AF:

0.0246

AC:

376

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0450

AC:

156

AN:

3468

East Asian (EAS)

AF:

0.186

AC:

966

AN:

5180

South Asian (SAS)

AF:

0.0554

AC:

267

AN:

4820

European-Finnish (FIN)

AF:

0.0168

AC:

178

AN:

10592

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0354

AC:

2407

AN:

68010

Other (OTH)

AF:

0.0360

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

231

462

693

924

1155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0368

Hom.:

225

Bravo

AF:

0.0354

Asia WGS

AF:

0.103

AC:

359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

2.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.97

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over