rs1344189

Variant summary

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

The NM_015460.4(MYRIP):​c.1666-2101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,990 control chromosomes in the GnomAD database, including 16,750 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 0.46 ( 16750 hom., cov: 33)

Consequence

MYRIP
NM_015460.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76
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]
EIF1B-AS1 (HGNC:44555): (EIF1B antisense RNA 1)

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 (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYRIPNM_015460.4 linkuse as main transcriptc.1666-2101C>T intron_variant ENST00000302541.11
EIF1B-AS1NR_033965.1 linkuse as main transcriptn.537-33031G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYRIPENST00000302541.11 linkuse as main transcriptc.1666-2101C>T intron_variant 1 NM_015460.4 P1Q8NFW9-1
EIF1B-AS1ENST00000657703.1 linkuse as main transcriptn.91-90017G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.456
AC:
69295
AN:
151872
Hom.:
16740
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.302
Gnomad AMI
AF:
0.455
Gnomad AMR
AF:
0.490
Gnomad ASJ
AF:
0.381
Gnomad EAS
AF:
0.265
Gnomad SAS
AF:
0.333
Gnomad FIN
AF:
0.582
Gnomad MID
AF:
0.379
Gnomad NFE
AF:
0.551
Gnomad OTH
AF:
0.431
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.456
AC:
69346
AN:
151990
Hom.:
16750
Cov.:
33
AF XY:
0.456
AC XY:
33896
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.302
Gnomad4 AMR
AF:
0.491
Gnomad4 ASJ
AF:
0.381
Gnomad4 EAS
AF:
0.265
Gnomad4 SAS
AF:
0.332
Gnomad4 FIN
AF:
0.582
Gnomad4 NFE
AF:
0.551
Gnomad4 OTH
AF:
0.428
Alfa
AF:
0.523
Hom.:
28954
Bravo
AF:
0.442
Asia WGS
AF:
0.289
AC:
1003
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.11
DANN
Benign
0.33

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.

Other links and lift over

dbSNP: rs1344189; hg19: chr3-40249244; API