dbSNP rs2679798: MYRIP:c.1666-63G>A (chr3-40209791-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015460.4(MYRIP):c.1666-63G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 1,594,510 control chromosomes in the GnomAD database, including 209,185 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 0.40 ( 15010 hom., cov: 31)

Exomes 𝑓: 0.51 ( 194175 hom. )

Consequence

MYRIP
NM_015460.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.475

Publications

15 publications found

Variant links:

Genes affected

MYRIP (HGNC:19156): (myosin VIIA and Rab interacting protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be involved in positive regulation of insulin secretion. Predicted to be located in actin cytoskeleton; dense core granule; and perinuclear region of cytoplasm. Predicted to be part of exocyst. Predicted to be active in cortical actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

MYRIP links:

EIF1B-AS1 (HGNC:):

EIF1B-AS1 links:

EIF1B-AS1 (HGNC:44555): (EIF1B antisense RNA 1)

EIF1B-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015460.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MYRIP	NM_015460.4	MANE Select	c.1666-63G>A	intron	N/A	NP_056275.2
MYRIP	NM_001284423.2		c.1666-63G>A	intron	N/A	NP_001271352.1
MYRIP	NM_001284424.2		c.1666-63G>A	intron	N/A	NP_001271353.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MYRIP	ENST00000302541.11	TSL:1 MANE Select	c.1666-63G>A	intron	N/A	ENSP00000301972.6
MYRIP	ENST00000444716.5	TSL:1	c.1666-63G>A	intron	N/A	ENSP00000398665.1
MYRIP	ENST00000396217.7	TSL:1	c.1399-63G>A	intron	N/A	ENSP00000379519.3

Frequencies

GnomAD3 genomes

AF:

0.403

AC:

61193

AN:

151826

Hom.:

15004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.457

Gnomad AMR

AF:

0.469

Gnomad ASJ

AF:

0.376

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.581

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.390

GnomAD4 exome

AF:

0.509

AC:

734572

AN:

1442564

Hom.:

194175

AF XY:

0.505

AC XY:

361838

AN XY:

716200

show subpopulations

African (AFR)

AF:

0.103

AC:

3381

AN:

32750

American (AMR)

AF:

0.508

AC:

21514

AN:

42358

Ashkenazi Jewish (ASJ)

AF:

0.368

AC:

9173

AN:

24902

East Asian (EAS)

AF:

0.286

AC:

11318

AN:

39534

South Asian (SAS)

AF:

0.341

AC:

28285

AN:

82984

European-Finnish (FIN)

AF:

0.573

AC:

30122

AN:

52558

Middle Eastern (MID)

AF:

0.369

AC:

2072

AN:

5612

European-Non Finnish (NFE)

AF:

0.545

AC:

601164

AN:

1102386

Other (OTH)

AF:

0.463

AC:

27543

AN:

59480

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

17743

35486

53228

70971

88714

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16650

33300

49950

66600

83250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.403

AC:

61207

AN:

151946

Hom.:

15010

Cov.:

AF XY:

0.404

AC XY:

30011

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.119

AC:

4919

AN:

41464

American (AMR)

AF:

0.470

AC:

7171

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.376

AC:

1304

AN:

3470

East Asian (EAS)

AF:

0.266

AC:

1367

AN:

5146

South Asian (SAS)

AF:

0.331

AC:

1594

AN:

4812

European-Finnish (FIN)

AF:

0.581

AC:

6122

AN:

10532

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.550

AC:

37391

AN:

67956

Other (OTH)

AF:

0.388

AC:

819

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1592

3183

4775

6366

7958

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

558

1116

1674

2232

2790

<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:

0.460

Hom.:

2980

Bravo

AF:

0.381

Asia WGS

AF:

0.274

AC:

951

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.4

(source)

DANN

Benign

0.54

PhyloP100

0.47

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over